noone@mail.com Analysis of Dieting study 16S data % Fri Sep 7 05:46:18 2018

(1.1.1.3.3) Plots of Abundance.

Plots are shown with relation to various combinations of meta data variables and in different graphical representations. Lots of plots here.

(1.1.1.3.3.2) Iterating over all combinations of grouping variables
(1.1.1.3.3.2.1) Grouping variables Sample.type,visit
(1.1.1.3.3.2.2) Iterating over Abundance. profile sorting order
(1.1.1.3.3.2.2.1) Abundance. profile sorting order: average abundance
(1.1.1.3.3.2.2.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.3.3.2.2.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.2.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.2.2.1.1.0) Table 37. Data table used for plots. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.2.2.1.1.0-3237b5a8742.1.1.1.3.3.2.2.2.1.1.csv

.record.id Sample.type visit feature Abundance
SM1 patient 1 Bacteroides 7.735e-01
SM10 patient 3 Bacteroides 2.364e-01
SM100 patient 4 Bacteroides 5.420e-01
SM11 patient 2 Bacteroides 8.578e-01
SM12 patient 1 Bacteroides 8.674e-01
SM13 patient 1 Bacteroides 4.295e-01
SM14 patient 1 Bacteroides 3.976e-02
SM15 control 1 Bacteroides 4.120e-01
SM16 patient 4 Bacteroides 3.890e-01
SM17 patient 1 Bacteroides 8.130e-01
SM18 patient 2 Bacteroides 6.537e-01
SM19 patient 2 Bacteroides 2.221e-01
SM2 patient 1 Bacteroides 8.611e-01
SM20 control 1 Bacteroides 3.742e-01
SM21 patient 1 Bacteroides 4.490e-01
SM22 patient 1 Bacteroides 5.831e-01
SM23 patient 2 Bacteroides 2.796e-01
SM24 patient 1 Bacteroides 1.435e-01
SM25 patient 4 Bacteroides 4.520e-01
SM26 control 1 Bacteroides 5.242e-01
SM28 control 1 Bacteroides 2.194e-01
SM29 patient 3 Bacteroides 9.002e-01
SM3 patient 2 Bacteroides 2.542e-01
SM30 patient 4 Bacteroides 6.581e-02
SM31 control 2 Bacteroides 4.094e-01
SM33 patient 1 Bacteroides 1.747e-01
SM35 control 1 Bacteroides 6.247e-01
SM36 patient 4 Bacteroides 3.219e-04
SM37 control 1 Bacteroides 3.301e-01
SM38 patient 2 Bacteroides 9.828e-01
SM39 patient 1 Bacteroides 4.095e-01
SM40 patient 4 Bacteroides 6.908e-01
SM41 patient 1 Bacteroides 5.037e-01
SM42 patient 4 Bacteroides 6.901e-01
SM43 patient 4 Bacteroides 6.589e-01
SM44 control 1 Bacteroides 1.150e-02
SM45 patient 2 Bacteroides 0.000e+00
SM48 control 1 Bacteroides 3.247e-01
SM49 patient 1 Bacteroides 9.292e-01
SM5 patient 3 Bacteroides 5.313e-01
SM50 patient 3 Bacteroides 0.000e+00
SM51 patient 4 Bacteroides 7.122e-01
SM52 patient 1 Bacteroides 8.105e-02
SM53 patient 2 Bacteroides 3.305e-01
SM54 patient 3 Bacteroides 6.239e-01
SM55 control 1 Bacteroides 7.465e-02
SM56 patient 2 Bacteroides 1.958e-02
SM57 patient 1 Bacteroides 8.679e-01
SM58 patient 2 Bacteroides 2.592e-02
SM59 patient 3 Bacteroides 5.206e-02
SM60 patient 3 Bacteroides 8.428e-01
SM62 patient 1 Bacteroides 9.643e-01
SM63 control 1 Bacteroides 5.135e-01
SM64 patient 2 Bacteroides 6.977e-01
SM65 patient 3 Bacteroides 3.711e-01
SM66 control 1 Bacteroides 6.218e-01
SM67 patient 4 Bacteroides 5.778e-01
SM68 patient 4 Bacteroides 1.440e-01
SM69 patient 4 Bacteroides 8.051e-01
SM7 control 1 Bacteroides 2.126e-01
SM70 control 1 Bacteroides 6.327e-02
SM71 patient 3 Bacteroides 8.388e-01
SM72 control 1 Bacteroides 4.762e-03
SM73 patient 1 Bacteroides 8.108e-01
SM74 control 2 Bacteroides 8.216e-02
SM75 patient 3 Bacteroides 2.377e-03
SM76 control 1 Bacteroides 8.153e-01
SM77 patient 2 Bacteroides 7.039e-01
SM79 patient 2 Bacteroides 1.173e-01
SM8 patient 1 Bacteroides 7.723e-01
SM81 control 1 Bacteroides 0.000e+00
SM82 patient 4 Bacteroides 8.624e-01
SM83 patient 1 Bacteroides 8.199e-01
SM84 patient 1 Bacteroides 2.885e-01
SM86 patient 2 Bacteroides 2.482e-03
SM87 patient 1 Bacteroides 5.438e-01
SM88 patient 2 Bacteroides 7.940e-01
SM89 control 1 Bacteroides 2.115e-03
SM9 patient 2 Bacteroides 6.096e-01
SM90 patient 2 Bacteroides 4.088e-01
SM91 patient 3 Bacteroides 6.525e-01
SM92 patient 3 Bacteroides 7.921e-01
SM93 patient 1 Bacteroides 6.404e-01
SM95 control 1 Bacteroides 4.955e-01
SM96 patient 1 Bacteroides 6.375e-01
SM98 patient 3 Bacteroides 2.848e-01
SM99 patient 3 Bacteroides 6.503e-01
SM1 patient 1 Prevotella 2.598e-04
SM10 patient 3 Prevotella 0.000e+00
SM100 patient 4 Prevotella 7.692e-05
SM11 patient 2 Prevotella 3.477e-04
SM12 patient 1 Prevotella 1.328e-04
SM13 patient 1 Prevotella 1.652e-02
SM14 patient 1 Prevotella 1.855e-02
SM15 control 1 Prevotella 1.415e-04
SM16 patient 4 Prevotella 0.000e+00
SM17 patient 1 Prevotella 4.137e-04
SM18 patient 2 Prevotella 3.357e-04
SM19 patient 2 Prevotella 2.314e-03
SM2 patient 1 Prevotella 2.480e-04
SM20 control 1 Prevotella 0.000e+00
SM21 patient 1 Prevotella 0.000e+00
SM22 patient 1 Prevotella 0.000e+00
SM23 patient 2 Prevotella 0.000e+00
SM24 patient 1 Prevotella 6.822e-01
SM25 patient 4 Prevotella 0.000e+00
SM26 control 1 Prevotella 2.758e-04
SM28 control 1 Prevotella 3.997e-04
SM29 patient 3 Prevotella 0.000e+00
SM3 patient 2 Prevotella 4.458e-02
SM30 patient 4 Prevotella 2.762e-03
SM31 control 2 Prevotella 1.618e-03
SM33 patient 1 Prevotella 0.000e+00
SM35 control 1 Prevotella 2.046e-03
SM36 patient 4 Prevotella 0.000e+00
SM37 control 1 Prevotella 7.741e-04
SM38 patient 2 Prevotella 1.028e-04
SM39 patient 1 Prevotella 4.073e-01
SM40 patient 4 Prevotella 2.775e-04
SM41 patient 1 Prevotella 0.000e+00
SM42 patient 4 Prevotella 4.994e-04
SM43 patient 4 Prevotella 7.452e-05
SM44 control 1 Prevotella 3.227e-01
SM45 patient 2 Prevotella 0.000e+00
SM48 control 1 Prevotella 2.151e-03
SM49 patient 1 Prevotella 0.000e+00
SM5 patient 3 Prevotella 5.950e-02
SM50 patient 3 Prevotella 0.000e+00
SM51 patient 4 Prevotella 2.231e-04
SM52 patient 1 Prevotella 8.062e-03
SM53 patient 2 Prevotella 4.611e-01
SM54 patient 3 Prevotella 0.000e+00
SM55 control 1 Prevotella 6.747e-01
SM56 patient 2 Prevotella 0.000e+00
SM57 patient 1 Prevotella 3.600e-04
SM58 patient 2 Prevotella 6.582e-01
SM59 patient 3 Prevotella 0.000e+00
SM60 patient 3 Prevotella 3.404e-04
SM62 patient 1 Prevotella 0.000e+00
SM63 control 1 Prevotella 2.703e-03
SM64 patient 2 Prevotella 1.113e-04
SM65 patient 3 Prevotella 1.374e-04
SM66 control 1 Prevotella 2.198e-04
SM67 patient 4 Prevotella 0.000e+00
SM68 patient 4 Prevotella 2.586e-02
SM69 patient 4 Prevotella 3.108e-04
SM7 control 1 Prevotella 0.000e+00
SM70 control 1 Prevotella 4.438e-01
SM71 patient 3 Prevotella 1.723e-03
SM72 control 1 Prevotella 2.651e-01
SM73 patient 1 Prevotella 1.009e-04
SM74 control 2 Prevotella 6.547e-04
SM75 patient 3 Prevotella 0.000e+00
SM76 control 1 Prevotella 5.743e-05
SM77 patient 2 Prevotella 1.127e-04
SM79 patient 2 Prevotella 6.782e-01
SM8 patient 1 Prevotella 7.416e-04
SM81 control 1 Prevotella 0.000e+00
SM82 patient 4 Prevotella 2.141e-04
SM83 patient 1 Prevotella 0.000e+00
SM84 patient 1 Prevotella 4.502e-01
SM86 patient 2 Prevotella 3.103e-04
SM87 patient 1 Prevotella 1.804e-01
SM88 patient 2 Prevotella 1.705e-04
SM89 control 1 Prevotella 8.603e-01
SM9 patient 2 Prevotella 8.227e-04
SM90 patient 2 Prevotella 5.776e-03
SM91 patient 3 Prevotella 2.212e-04
SM92 patient 3 Prevotella 9.411e-02
SM93 patient 1 Prevotella 0.000e+00
SM95 control 1 Prevotella 0.000e+00
SM96 patient 1 Prevotella 0.000e+00
SM98 patient 3 Prevotella 5.140e-01
SM99 patient 3 Prevotella 4.757e-04
SM1 patient 1 Unclassified_Lachnospiraceae 4.529e-02
SM10 patient 3 Unclassified_Lachnospiraceae 2.607e-01
SM100 patient 4 Unclassified_Lachnospiraceae 1.308e-01
SM11 patient 2 Unclassified_Lachnospiraceae 4.404e-03
SM12 patient 1 Unclassified_Lachnospiraceae 1.049e-02
SM13 patient 1 Unclassified_Lachnospiraceae 1.116e-02
SM14 patient 1 Unclassified_Lachnospiraceae 6.172e-02
SM15 control 1 Unclassified_Lachnospiraceae 5.053e-02
SM16 patient 4 Unclassified_Lachnospiraceae 1.583e-01
SM17 patient 1 Unclassified_Lachnospiraceae 2.938e-02
SM18 patient 2 Unclassified_Lachnospiraceae 5.271e-02
SM19 patient 2 Unclassified_Lachnospiraceae 1.055e-01
SM2 patient 1 Unclassified_Lachnospiraceae 1.097e-02
SM20 control 1 Unclassified_Lachnospiraceae 2.256e-02
SM21 patient 1 Unclassified_Lachnospiraceae 5.532e-02
SM22 patient 1 Unclassified_Lachnospiraceae 1.113e-01
SM23 patient 2 Unclassified_Lachnospiraceae 4.148e-04
SM24 patient 1 Unclassified_Lachnospiraceae 1.402e-02
SM25 patient 4 Unclassified_Lachnospiraceae 8.430e-02
SM26 control 1 Unclassified_Lachnospiraceae 7.501e-02
SM28 control 1 Unclassified_Lachnospiraceae 9.952e-02
SM29 patient 3 Unclassified_Lachnospiraceae 1.128e-02
SM3 patient 2 Unclassified_Lachnospiraceae 1.560e-01
SM30 patient 4 Unclassified_Lachnospiraceae 3.297e-01
SM31 control 2 Unclassified_Lachnospiraceae 1.294e-02
SM33 patient 1 Unclassified_Lachnospiraceae 3.934e-03

(1.1.1.3.3.2.2.2.1.1.1) Widget 38. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.2.2.1.1.1-323552a4c8Dynamic.Pivot.Table.html

(1.1.1.3.3.2.2.2.1.1.1) Widget 39. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.2.2.1.1.1-32324020e98Dynamic.Pivot.Table.html

(1.1.1.3.3.2.2.2.1.1.1) Table 38. Summary table. Data grouped by Sample.type,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.2.2.1.1.1-3237a17f021.1.1.1.3.3.2.2.2.1.1.csv

feature Sample.type visit mean sd median incidence
Bacteroides control 1 3.125e-01 0.2538464 3.274e-01 0.94444
Bacteroides control 2 2.458e-01 0.2313828 2.458e-01 1.00000
Bacteroides patient 1 5.828e-01 0.2873867 6.375e-01 1.00000
Bacteroides patient 2 4.094e-01 0.3304484 3.305e-01 0.94118
Bacteroides patient 3 4.842e-01 0.3242795 5.776e-01 0.92857
Bacteroides patient 4 5.070e-01 0.2819563 5.778e-01 1.00000
Prevotella control 1 1.431e-01 0.2654918 5.869e-04 0.77778
Prevotella control 2 1.136e-03 0.0006813 1.136e-03 1.00000
Prevotella patient 1 7.676e-02 0.1823681 2.480e-04 0.60870
Prevotella patient 2 1.090e-01 0.2379624 3.357e-04 0.82353
Prevotella patient 3 4.789e-02 0.1371393 1.793e-04 0.57143
Prevotella patient 4 2.331e-03 0.0071093 2.141e-04 0.69231
Unclassified_Lachnospiraceae control 1 6.389e-02 0.0412008 6.129e-02 1.00000
Unclassified_Lachnospiraceae control 2 6.654e-02 0.0757919 6.654e-02 1.00000
Unclassified_Lachnospiraceae patient 1 2.933e-02 0.0314771 1.135e-02 0.95652
Unclassified_Lachnospiraceae patient 2 4.774e-02 0.0603731 2.660e-02 0.94118
Unclassified_Lachnospiraceae patient 3 9.946e-02 0.1218097 4.278e-02 1.00000
Unclassified_Lachnospiraceae patient 4 8.700e-02 0.0868167 5.327e-02 1.00000
Faecalibacterium control 1 4.217e-02 0.0440054 3.575e-02 0.94444
Faecalibacterium control 2 3.452e-02 0.0442349 3.452e-02 1.00000
Faecalibacterium patient 1 2.729e-02 0.0297587 2.047e-02 0.95652
Faecalibacterium patient 2 5.994e-02 0.1135543 1.526e-02 0.88235
Faecalibacterium patient 3 3.536e-02 0.0397725 2.075e-02 1.00000
Faecalibacterium patient 4 6.643e-02 0.0771098 3.868e-02 1.00000
Lachnospiracea_incertae_sedis control 1 3.238e-02 0.0266386 2.788e-02 0.94444
Lachnospiracea_incertae_sedis control 2 5.683e-02 0.0797987 5.683e-02 1.00000
Lachnospiracea_incertae_sedis patient 1 1.017e-02 0.0113133 4.911e-03 0.91304
Lachnospiracea_incertae_sedis patient 2 3.467e-02 0.0451511 1.592e-02 0.88235
Lachnospiracea_incertae_sedis patient 3 5.461e-02 0.0741321 1.830e-02 0.92857
Lachnospiracea_incertae_sedis patient 4 5.532e-02 0.0598858 5.855e-02 0.92308
Parabacteroides control 1 8.828e-03 0.0080690 6.610e-03 0.94444
Parabacteroides control 2 1.807e-02 0.0190712 1.807e-02 1.00000
Parabacteroides patient 1 3.735e-02 0.1051873 2.651e-03 0.73913
Parabacteroides patient 2 5.616e-02 0.1713182 8.295e-04 0.82353
Parabacteroides patient 3 3.337e-02 0.0584943 4.370e-03 0.64286
Parabacteroides patient 4 3.474e-02 0.0922398 2.231e-04 0.69231
Alistipes control 1 4.359e-02 0.0743642 1.748e-02 0.77778
Alistipes control 2 6.305e-02 0.0836085 6.305e-02 1.00000
Alistipes patient 1 3.249e-02 0.0560977 9.784e-03 0.69565
Alistipes patient 2 2.111e-02 0.0418863 0.000e+00 0.47059
Alistipes patient 3 6.408e-03 0.0158919 0.000e+00 0.42857
Alistipes patient 4 7.073e-03 0.0117754 8.319e-04 0.53846
Blautia control 1 2.657e-02 0.0444930 1.644e-02 1.00000
Blautia control 2 4.533e-02 0.0618126 4.533e-02 1.00000
Blautia patient 1 1.235e-02 0.0164027 4.067e-03 0.95652
Blautia patient 2 1.868e-02 0.0333637 3.861e-03 0.82353
Blautia patient 3 2.365e-02 0.0274097 1.545e-02 1.00000
Blautia patient 4 1.464e-02 0.0193524 6.334e-03 1.00000
Ruminococcus control 1 5.576e-02 0.0872197 2.428e-02 0.94444
Ruminococcus control 2 1.140e-01 0.1423975 1.140e-01 1.00000
Ruminococcus patient 1 5.175e-03 0.0091511 1.893e-03 0.91304
Ruminococcus patient 2 5.007e-03 0.0085975 1.510e-03 0.76471
Ruminococcus patient 3 1.107e-02 0.0216317 2.787e-03 0.85714
Ruminococcus patient 4 6.834e-03 0.0137693 1.988e-03 0.76923
Unclassified_Clostridiales control 1 1.825e-02 0.0216929 1.279e-02 0.94444
Unclassified_Clostridiales control 2 3.991e-02 0.0204012 3.991e-02 1.00000
Unclassified_Clostridiales patient 1 1.119e-02 0.0142830 7.085e-03 1.00000
Unclassified_Clostridiales patient 2 9.744e-03 0.0119547 6.365e-03 0.88235
Unclassified_Clostridiales patient 3 3.047e-02 0.0653628 1.140e-02 1.00000
Unclassified_Clostridiales patient 4 1.318e-02 0.0159711 6.475e-03 1.00000
Lactobacillus control 1 1.522e-02 0.0641403 0.000e+00 0.27778
Lactobacillus control 2 0.000e+00 0.0000000 0.000e+00 0.00000
Lactobacillus patient 1 3.493e-04 0.0011589 0.000e+00 0.17391
Lactobacillus patient 2 5.878e-02 0.2418040 0.000e+00 0.29412
Lactobacillus patient 3 3.806e-04 0.0012664 0.000e+00 0.21429
Lactobacillus patient 4 5.014e-04 0.0015281 0.000e+00 0.23077
Unclassified_Ruminococcaceae control 1 3.224e-02 0.0335651 1.940e-02 0.94444
Unclassified_Ruminococcaceae control 2 5.710e-02 0.0451079 5.710e-02 1.00000
Unclassified_Ruminococcaceae patient 1 1.240e-02 0.0253701 6.698e-03 1.00000
Unclassified_Ruminococcaceae patient 2 6.016e-03 0.0085811 2.816e-03 0.88235
Unclassified_Ruminococcaceae patient 3 5.898e-03 0.0076353 3.294e-03 1.00000
Unclassified_Ruminococcaceae patient 4 8.677e-03 0.0119062 2.538e-03 1.00000
Roseburia control 1 9.054e-03 0.0069943 6.302e-03 1.00000
Roseburia control 2 1.069e-02 0.0071054 1.069e-02 1.00000
Roseburia patient 1 5.268e-03 0.0062277 2.966e-03 0.86957
Roseburia patient 2 1.656e-02 0.0256221 4.243e-03 0.94118
Roseburia patient 3 1.476e-02 0.0161405 1.115e-02 1.00000
Roseburia patient 4 3.631e-02 0.0373736 2.288e-02 1.00000
Clostridium_XI control 1 9.259e-03 0.0108630 6.425e-03 0.94444
Clostridium_XI control 2 1.387e-02 0.0081666 1.387e-02 1.00000
Clostridium_XI patient 1 1.741e-02 0.0457103 2.423e-03 0.82609
Clostridium_XI patient 2 1.178e-02 0.0350550 1.438e-03 0.76471
Clostridium_XI patient 3 6.773e-03 0.0091778 2.379e-03 0.92857
Clostridium_XI patient 4 2.371e-02 0.0353583 7.158e-03 1.00000
Enterococcus control 1 3.133e-03 0.0131693 0.000e+00 0.16667
Enterococcus control 2 3.437e-03 0.0048606 3.437e-03 0.50000
Enterococcus patient 1 3.391e-03 0.0149272 0.000e+00 0.34783
Enterococcus patient 2 4.222e-02 0.1722129 0.000e+00 0.41176
Enterococcus patient 3 2.815e-04 0.0005849 0.000e+00 0.28571
Enterococcus patient 4 3.035e-04 0.0006924 0.000e+00 0.23077
Erysipelotrichaceae_incertae_sedis control 1 1.177e-03 0.0016041 6.149e-04 0.77778
Erysipelotrichaceae_incertae_sedis control 2 8.955e-04 0.0001223 8.955e-04 1.00000
Erysipelotrichaceae_incertae_sedis patient 1 2.007e-02 0.0799902 1.212e-03 0.73913
Erysipelotrichaceae_incertae_sedis patient 2 1.738e-03 0.0028560 4.125e-04 0.82353
Erysipelotrichaceae_incertae_sedis patient 3 9.515e-03 0.0139050 2.854e-03 1.00000
Erysipelotrichaceae_incertae_sedis patient 4 1.522e-02 0.0500792 9.325e-04 0.84615
Megamonas control 1 1.856e-02 0.0528681 0.000e+00 0.16667
Megamonas control 2 0.000e+00 0.0000000 0.000e+00 0.00000
Megamonas patient 1 2.174e-03 0.0104047 0.000e+00 0.08696
Megamonas patient 2 1.961e-02 0.0573116 0.000e+00 0.11765
Megamonas patient 3 2.782e-03 0.0104102 0.000e+00 0.07143
Megamonas patient 4 2.288e-03 0.0078271 0.000e+00 0.15385
Sutterella control 1 1.005e-02 0.0274571 1.351e-03 0.61111
Sutterella control 2 0.000e+00 0.0000000 0.000e+00 0.00000
Sutterella patient 1 6.547e-03 0.0148652 4.426e-05 0.52174
Sutterella patient 2 7.151e-03 0.0134897 0.000e+00 0.29412
Sutterella patient 3 5.046e-03 0.0127503 0.000e+00 0.21429
Sutterella patient 4 1.018e-02 0.0244892 0.000e+00 0.30769
Escherichia_Shigella control 1 1.014e-02 0.0395132 3.219e-04 0.55556
Escherichia_Shigella control 2 4.045e-04 0.0005721 4.045e-04 0.50000
Escherichia_Shigella patient 1 1.410e-02 0.0440606 0.000e+00 0.39130
Escherichia_Shigella patient 2 3.576e-04 0.0012975 0.000e+00 0.29412
Escherichia_Shigella patient 3 2.356e-03 0.0051551 3.234e-04 0.64286
Escherichia_Shigella patient 4 7.543e-03 0.0172863 8.323e-05 0.53846
Unclassified_Bacteria control 1 1.364e-02 0.0114079 1.054e-02 1.00000
Unclassified_Bacteria control 2 2.617e-02 0.0324305 2.617e-02 1.00000
Unclassified_Bacteria patient 1 8.586e-03 0.0185047 3.658e-03 0.95652
Unclassified_Bacteria patient 2 2.162e-03 0.0019168 1.958e-03 0.88235
Unclassified_Bacteria patient 3 3.391e-03 0.0031220 2.417e-03 1.00000
Unclassified_Bacteria patient 4 4.709e-03 0.0065490 1.415e-03 1.00000
Clostridium_IV control 1 1.258e-02 0.0141985 5.803e-03 0.94444
Clostridium_IV control 2 8.200e-02 0.0659652 8.200e-02 1.00000
Clostridium_IV patient 1 5.157e-03 0.0087292 1.461e-03 0.82609
Clostridium_IV patient 2 1.862e-03 0.0035789 2.569e-04 0.58824
Clostridium_IV patient 3 1.834e-03 0.0036717 3.273e-04 0.64286
Clostridium_IV patient 4 4.154e-03 0.0104238 3.219e-04 0.69231
Clostridium_XlVa control 1 8.736e-03 0.0124426 4.491e-03 0.94444
Clostridium_XlVa control 2 4.689e-03 0.0026269 4.689e-03 1.00000
Clostridium_XlVa patient 1 6.183e-03 0.0072269 4.820e-03 0.95652
Clostridium_XlVa patient 2 2.457e-03 0.0026715 1.468e-03 0.94118
Clostridium_XlVa patient 3 1.005e-02 0.0164355 2.887e-03 1.00000
Clostridium_XlVa patient 4 7.189e-03 0.0056921 6.764e-03 0.92308
Unclassified_Firmicutes control 1 8.036e-03 0.0109414 3.210e-03 1.00000
Unclassified_Firmicutes control 2 1.259e-02 0.0057974 1.259e-02 1.00000
Unclassified_Firmicutes patient 1 2.429e-03 0.0033961 8.410e-04 0.86957
Unclassified_Firmicutes patient 2 5.485e-03 0.0092386 7.794e-04 0.76471
Unclassified_Firmicutes patient 3 9.325e-03 0.0180189 1.689e-03 1.00000
Unclassified_Firmicutes patient 4 4.155e-03 0.0066088 9.688e-04 0.92308
Haemophilus control 1 8.739e-04 0.0012254 2.922e-04 0.66667
Haemophilus control 2 4.910e-03 0.0069438 4.910e-03 0.50000
Haemophilus patient 1 5.492e-04 0.0016996 0.000e+00 0.34783
Haemophilus patient 2 1.329e-03 0.0020544 1.127e-04 0.58824
Haemophilus patient 3 6.978e-03 0.0142668 5.086e-04 0.50000
Haemophilus patient 4 2.192e-02 0.0530352 2.236e-04 0.76923
Bifidobacterium control 1 1.565e-02 0.0449947 1.592e-03 0.77778
Bifidobacterium control 2 6.749e-03 0.0089723 6.749e-03 1.00000
Bifidobacterium patient 1 1.791e-03 0.0046990 3.015e-04 0.65217
Bifidobacterium patient 2 7.066e-04 0.0018786 5.138e-05 0.52941
Bifidobacterium patient 3 3.665e-03 0.0070439 1.831e-04 0.57143
Bifidobacterium patient 4 2.813e-03 0.0050442 2.231e-04 0.61538
Dorea control 1 8.060e-03 0.0090249 4.976e-03 0.94444
Dorea control 2 1.137e-02 0.0052122 1.137e-02 1.00000
Dorea patient 1 4.921e-03 0.0096203 1.112e-03 0.73913
Dorea patient 2 1.453e-03 0.0018565 8.393e-04 0.82353
Dorea patient 3 6.028e-03 0.0104849 1.281e-03 0.85714
Dorea patient 4 2.899e-03 0.0058484 6.232e-04 0.92308
Unclassified_Bacteroidales control 1 2.201e-03 0.0039404 1.271e-03 0.83333
Unclassified_Bacteroidales control 2 1.502e-03 0.0007359 1.502e-03 1.00000
Unclassified_Bacteroidales patient 1 6.359e-03 0.0137559 2.017e-03 1.00000
Unclassified_Bacteroidales patient 2 8.760e-03 0.0201346 1.942e-03 0.88235
Unclassified_Bacteroidales patient 3 2.801e-03 0.0035044 2.015e-03 0.71429
Unclassified_Bacteroidales patient 4 1.617e-03 0.0022822 5.550e-04 0.76923
Clostridium_XVIII control 1 4.144e-03 0.0102711 1.151e-03 0.88889
Clostridium_XVIII control 2 6.741e-03 0.0030526 6.741e-03 1.00000
Clostridium_XVIII patient 1 3.581e-03 0.0042045 1.786e-03 0.86957
Clostridium_XVIII patient 2 1.424e-03 0.0031420 4.636e-04 0.76471
Clostridium_XVIII patient 3 6.793e-03 0.0151982 8.433e-04 0.78571
Clostridium_XVIII patient 4 6.920e-03 0.0169633 1.387e-03 0.92308
Akkermansia control 1 2.550e-03 0.0051198 0.000e+00 0.38889
Akkermansia control 2 2.136e-02 0.0292859 2.136e-02 1.00000
Akkermansia patient 1 1.056e-02 0.0368541 0.000e+00 0.34783
Akkermansia patient 2 3.903e-04 0.0011122 0.000e+00 0.11765
Akkermansia patient 3 5.727e-04 0.0018438 0.000e+00 0.14286
Akkermansia patient 4 2.846e-05 0.0001026 0.000e+00 0.07692
Veillonella control 1 1.392e-03 0.0051949 0.000e+00 0.33333
Veillonella control 2 4.910e-04 0.0006944 4.910e-04 0.50000
Veillonella patient 1 1.094e-03 0.0036140 0.000e+00 0.47826
Veillonella patient 2 6.980e-03 0.0192133 1.957e-04 0.64706
Veillonella patient 3 7.884e-03 0.0225365 4.661e-04 0.64286
Veillonella patient 4 1.499e-03 0.0029191 1.554e-04 0.69231
Streptococcus control 1 5.433e-03 0.0178726 3.570e-04 0.77778
Streptococcus control 2 1.541e-03 0.0012534 1.541e-03 1.00000
Streptococcus patient 1 2.134e-03 0.0048585 1.009e-04 0.69565
Streptococcus patient 2 1.752e-03 0.0031860 2.816e-04 0.70588
Streptococcus patient 3 5.250e-03 0.0163790 3.668e-04 0.71429
Streptococcus patient 4 1.655e-03 0.0028281 3.077e-04 0.92308
Clostridium_sensu_stricto control 1 3.142e-03 0.0073249 2.614e-04 0.72222
Clostridium_sensu_stricto control 2 3.303e-03 0.0018102 3.303e-03 1.00000
Clostridium_sensu_stricto patient 1 3.344e-03 0.0072111 6.071e-05 0.52174
Clostridium_sensu_stricto patient 2 1.329e-03 0.0047976 0.000e+00 0.35294
Clostridium_sensu_stricto patient 3 5.140e-03 0.0111072 9.659e-04 0.64286
Clostridium_sensu_stricto patient 4 2.817e-03 0.0044321 5.550e-04 0.61538
Unclassified_Clostridiaceae_1 control 1 5.124e-04 0.0013443 2.871e-05 0.50000
Unclassified_Clostridiaceae_1 control 2 1.830e-03 0.0002729 1.830e-03 1.00000
Unclassified_Clostridiaceae_1 patient 1 2.751e-04 0.0006520 0.000e+00 0.34783
Unclassified_Clostridiaceae_1 patient 2 5.875e-04 0.0021706 0.000e+00 0.35294
Unclassified_Clostridiaceae_1 patient 3 1.194e-02 0.0340117 5.139e-04 0.57143
Unclassified_Clostridiaceae_1 patient 4 3.902e-03 0.0118332 1.554e-04 0.53846
Klebsiella control 1 5.130e-03 0.0215002 0.000e+00 0.16667
Klebsiella control 2 0.000e+00 0.0000000 0.000e+00 0.00000

(1.1.1.3.3.2.2.2.1.1.1) Figure 120. Abundance. Data grouped by Sample.type,visit. bar_stacked plot. Image file: plots/323471e1474.svg.

(1.1.1.3.3.2.2.2.1.1.1) Figure 121. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323a72514d.svg.

(1.1.1.3.3.2.2.2.1.1.1) Figure 122. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3237bf6fa0f.svg.

(1.1.1.3.3.2.2.2.1.1.1) Figure 123. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32317dffe9e.svg.

(1.1.1.3.3.2.2.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.2.2.1.2.1) Figure 124. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323407ddd9c.svg.

(1.1.1.3.3.2.2.2.1.2.1) Figure 125. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/323182452f9.svg.

(1.1.1.3.3.2.2.2.1.2.1) Figure 126. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/32328458021.svg.

(1.1.1.3.3.2.2.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.2.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.2.2.2.1.1) Figure 127. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/32318ea7169.svg.

(1.1.1.3.3.2.2.2.2.1.1) Figure 128. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/3232e9cd17.svg.

(1.1.1.3.3.2.2.2.2.1.1) Figure 129. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323424673bc.svg.

(1.1.1.3.3.2.2.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.2.2.2.2.1) Figure 130. Abundance. Data grouped by Sample.type,visit. bar (sample mean) plot. Image file: plots/323dfcbe3.svg.

(1.1.1.3.3.2.2.2.2.2.1) Figure 131. Abundance. Data grouped by Sample.type,visit. violin plot. Image file: plots/32366afa571.svg.

(1.1.1.3.3.2.2.2.2.2.1) Figure 132. Abundance. Data grouped by Sample.type,visit. boxplot plot. Image file: plots/323aff79f0.svg.

(1.1.1.3.3.2.3) Grouping variables Sample.type.Drug.Before,visit
(1.1.1.3.3.2.4) Iterating over Abundance. profile sorting order
(1.1.1.3.3.2.4.1) Abundance. profile sorting order: average abundance
(1.1.1.3.3.2.4.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.3.3.2.4.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.4.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.4.2.1.1.0) Table 39. Data table used for plots. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.4.2.1.1.0-323727cf321.1.1.1.3.3.2.4.2.1.1.csv

.record.id Sample.type.Drug.Before visit feature Abundance
SM1 patient TRUE . 1 Bacteroides 7.735e-01
SM10 patient TRUE . 3 Bacteroides 2.364e-01
SM100 patient TRUE . 4 Bacteroides 5.420e-01
SM11 patient TRUE . 2 Bacteroides 8.578e-01
SM12 patient TRUE . 1 Bacteroides 8.674e-01
SM13 patient FALSE . 1 Bacteroides 4.295e-01
SM14 patient FALSE . 1 Bacteroides 3.976e-02
SM15 1 1 Bacteroides 4.120e-01
SM16 patient FALSE . 4 Bacteroides 3.890e-01
SM17 patient TRUE . 1 Bacteroides 8.130e-01
SM18 patient FALSE . 2 Bacteroides 6.537e-01
SM19 patient FALSE . 2 Bacteroides 2.221e-01
SM2 patient FALSE . 1 Bacteroides 8.611e-01
SM20 1 1 Bacteroides 3.742e-01
SM21 patient FALSE . 1 Bacteroides 4.490e-01
SM22 patient TRUE . 1 Bacteroides 5.831e-01
SM23 patient TRUE . 2 Bacteroides 2.796e-01
SM24 patient FALSE . 1 Bacteroides 1.435e-01
SM25 patient FALSE . 4 Bacteroides 4.520e-01
SM26 1 1 Bacteroides 5.242e-01
SM28 1 1 Bacteroides 2.194e-01
SM29 patient TRUE . 3 Bacteroides 9.002e-01
SM3 patient TRUE . 2 Bacteroides 2.542e-01
SM30 patient TRUE . 4 Bacteroides 6.581e-02
SM31 1 2 Bacteroides 4.094e-01
SM33 patient TRUE . 1 Bacteroides 1.747e-01
SM35 1 1 Bacteroides 6.247e-01
SM36 patient FALSE . 4 Bacteroides 3.219e-04
SM37 1 1 Bacteroides 3.301e-01
SM38 patient TRUE . 2 Bacteroides 9.828e-01
SM39 patient FALSE . 1 Bacteroides 4.095e-01
SM40 patient FALSE . 4 Bacteroides 6.908e-01
SM41 patient TRUE . 1 Bacteroides 5.037e-01
SM42 patient FALSE . 4 Bacteroides 6.901e-01
SM43 patient TRUE . 4 Bacteroides 6.589e-01
SM44 1 1 Bacteroides 1.150e-02
SM45 patient FALSE . 2 Bacteroides 0.000e+00
SM48 1 1 Bacteroides 3.247e-01
SM49 patient TRUE . 1 Bacteroides 9.292e-01
SM5 patient TRUE . 3 Bacteroides 5.313e-01
SM50 patient FALSE . 3 Bacteroides 0.000e+00
SM51 patient TRUE . 4 Bacteroides 7.122e-01
SM52 patient FALSE . 1 Bacteroides 8.105e-02
SM53 patient TRUE . 2 Bacteroides 3.305e-01
SM54 patient TRUE . 3 Bacteroides 6.239e-01
SM55 1 1 Bacteroides 7.465e-02
SM56 patient TRUE . 2 Bacteroides 1.958e-02
SM57 patient TRUE . 1 Bacteroides 8.679e-01
SM58 patient FALSE . 2 Bacteroides 2.592e-02
SM59 patient FALSE . 3 Bacteroides 5.206e-02
SM60 patient TRUE . 3 Bacteroides 8.428e-01
SM62 patient TRUE . 1 Bacteroides 9.643e-01
SM63 1 1 Bacteroides 5.135e-01
SM64 patient TRUE . 2 Bacteroides 6.977e-01
SM65 patient TRUE . 3 Bacteroides 3.711e-01
SM66 1 1 Bacteroides 6.218e-01
SM67 patient TRUE . 4 Bacteroides 5.778e-01
SM68 patient FALSE . 4 Bacteroides 1.440e-01
SM69 patient TRUE . 4 Bacteroides 8.051e-01
SM7 1 1 Bacteroides 2.126e-01
SM70 1 1 Bacteroides 6.327e-02
SM71 patient TRUE . 3 Bacteroides 8.388e-01
SM72 1 1 Bacteroides 4.762e-03
SM73 patient FALSE . 1 Bacteroides 8.108e-01
SM74 1 2 Bacteroides 8.216e-02
SM75 patient FALSE . 3 Bacteroides 2.377e-03
SM76 1 1 Bacteroides 8.153e-01
SM77 patient TRUE . 2 Bacteroides 7.039e-01
SM79 patient FALSE . 2 Bacteroides 1.173e-01
SM8 patient FALSE . 1 Bacteroides 7.723e-01
SM81 1 1 Bacteroides 0.000e+00
SM82 patient TRUE . 4 Bacteroides 8.624e-01
SM83 patient TRUE . 1 Bacteroides 8.199e-01
SM84 patient TRUE . 1 Bacteroides 2.885e-01
SM86 patient TRUE . 2 Bacteroides 2.482e-03
SM87 patient TRUE . 1 Bacteroides 5.438e-01
SM88 patient TRUE . 2 Bacteroides 7.940e-01
SM89 1 1 Bacteroides 2.115e-03
SM9 patient FALSE . 2 Bacteroides 6.096e-01
SM90 patient FALSE . 2 Bacteroides 4.088e-01
SM91 patient TRUE . 3 Bacteroides 6.525e-01
SM92 patient FALSE . 3 Bacteroides 7.921e-01
SM93 patient TRUE . 1 Bacteroides 6.404e-01
SM95 1 1 Bacteroides 4.955e-01
SM96 patient FALSE . 1 Bacteroides 6.375e-01
SM98 patient FALSE . 3 Bacteroides 2.848e-01
SM99 patient FALSE . 3 Bacteroides 6.503e-01
SM1 patient TRUE . 1 Prevotella 2.598e-04
SM10 patient TRUE . 3 Prevotella 0.000e+00
SM100 patient TRUE . 4 Prevotella 7.692e-05
SM11 patient TRUE . 2 Prevotella 3.477e-04
SM12 patient TRUE . 1 Prevotella 1.328e-04
SM13 patient FALSE . 1 Prevotella 1.652e-02
SM14 patient FALSE . 1 Prevotella 1.855e-02
SM15 1 1 Prevotella 1.415e-04
SM16 patient FALSE . 4 Prevotella 0.000e+00
SM17 patient TRUE . 1 Prevotella 4.137e-04
SM18 patient FALSE . 2 Prevotella 3.357e-04
SM19 patient FALSE . 2 Prevotella 2.314e-03
SM2 patient FALSE . 1 Prevotella 2.480e-04
SM20 1 1 Prevotella 0.000e+00
SM21 patient FALSE . 1 Prevotella 0.000e+00
SM22 patient TRUE . 1 Prevotella 0.000e+00
SM23 patient TRUE . 2 Prevotella 0.000e+00
SM24 patient FALSE . 1 Prevotella 6.822e-01
SM25 patient FALSE . 4 Prevotella 0.000e+00
SM26 1 1 Prevotella 2.758e-04
SM28 1 1 Prevotella 3.997e-04
SM29 patient TRUE . 3 Prevotella 0.000e+00
SM3 patient TRUE . 2 Prevotella 4.458e-02
SM30 patient TRUE . 4 Prevotella 2.762e-03
SM31 1 2 Prevotella 1.618e-03
SM33 patient TRUE . 1 Prevotella 0.000e+00
SM35 1 1 Prevotella 2.046e-03
SM36 patient FALSE . 4 Prevotella 0.000e+00
SM37 1 1 Prevotella 7.741e-04
SM38 patient TRUE . 2 Prevotella 1.028e-04
SM39 patient FALSE . 1 Prevotella 4.073e-01
SM40 patient FALSE . 4 Prevotella 2.775e-04
SM41 patient TRUE . 1 Prevotella 0.000e+00
SM42 patient FALSE . 4 Prevotella 4.994e-04
SM43 patient TRUE . 4 Prevotella 7.452e-05
SM44 1 1 Prevotella 3.227e-01
SM45 patient FALSE . 2 Prevotella 0.000e+00
SM48 1 1 Prevotella 2.151e-03
SM49 patient TRUE . 1 Prevotella 0.000e+00
SM5 patient TRUE . 3 Prevotella 5.950e-02
SM50 patient FALSE . 3 Prevotella 0.000e+00
SM51 patient TRUE . 4 Prevotella 2.231e-04
SM52 patient FALSE . 1 Prevotella 8.062e-03
SM53 patient TRUE . 2 Prevotella 4.611e-01
SM54 patient TRUE . 3 Prevotella 0.000e+00
SM55 1 1 Prevotella 6.747e-01
SM56 patient TRUE . 2 Prevotella 0.000e+00
SM57 patient TRUE . 1 Prevotella 3.600e-04
SM58 patient FALSE . 2 Prevotella 6.582e-01
SM59 patient FALSE . 3 Prevotella 0.000e+00
SM60 patient TRUE . 3 Prevotella 3.404e-04
SM62 patient TRUE . 1 Prevotella 0.000e+00
SM63 1 1 Prevotella 2.703e-03
SM64 patient TRUE . 2 Prevotella 1.113e-04
SM65 patient TRUE . 3 Prevotella 1.374e-04
SM66 1 1 Prevotella 2.198e-04
SM67 patient TRUE . 4 Prevotella 0.000e+00
SM68 patient FALSE . 4 Prevotella 2.586e-02
SM69 patient TRUE . 4 Prevotella 3.108e-04
SM7 1 1 Prevotella 0.000e+00
SM70 1 1 Prevotella 4.438e-01
SM71 patient TRUE . 3 Prevotella 1.723e-03
SM72 1 1 Prevotella 2.651e-01
SM73 patient FALSE . 1 Prevotella 1.009e-04
SM74 1 2 Prevotella 6.547e-04
SM75 patient FALSE . 3 Prevotella 0.000e+00
SM76 1 1 Prevotella 5.743e-05
SM77 patient TRUE . 2 Prevotella 1.127e-04
SM79 patient FALSE . 2 Prevotella 6.782e-01
SM8 patient FALSE . 1 Prevotella 7.416e-04
SM81 1 1 Prevotella 0.000e+00
SM82 patient TRUE . 4 Prevotella 2.141e-04
SM83 patient TRUE . 1 Prevotella 0.000e+00
SM84 patient TRUE . 1 Prevotella 4.502e-01
SM86 patient TRUE . 2 Prevotella 3.103e-04
SM87 patient TRUE . 1 Prevotella 1.804e-01
SM88 patient TRUE . 2 Prevotella 1.705e-04
SM89 1 1 Prevotella 8.603e-01
SM9 patient FALSE . 2 Prevotella 8.227e-04
SM90 patient FALSE . 2 Prevotella 5.776e-03
SM91 patient TRUE . 3 Prevotella 2.212e-04
SM92 patient FALSE . 3 Prevotella 9.411e-02
SM93 patient TRUE . 1 Prevotella 0.000e+00
SM95 1 1 Prevotella 0.000e+00
SM96 patient FALSE . 1 Prevotella 0.000e+00
SM98 patient FALSE . 3 Prevotella 5.140e-01
SM99 patient FALSE . 3 Prevotella 4.757e-04
SM1 patient TRUE . 1 Unclassified_Lachnospiraceae 4.529e-02
SM10 patient TRUE . 3 Unclassified_Lachnospiraceae 2.607e-01
SM100 patient TRUE . 4 Unclassified_Lachnospiraceae 1.308e-01
SM11 patient TRUE . 2 Unclassified_Lachnospiraceae 4.404e-03
SM12 patient TRUE . 1 Unclassified_Lachnospiraceae 1.049e-02
SM13 patient FALSE . 1 Unclassified_Lachnospiraceae 1.116e-02
SM14 patient FALSE . 1 Unclassified_Lachnospiraceae 6.172e-02
SM15 1 1 Unclassified_Lachnospiraceae 5.053e-02
SM16 patient FALSE . 4 Unclassified_Lachnospiraceae 1.583e-01
SM17 patient TRUE . 1 Unclassified_Lachnospiraceae 2.938e-02
SM18 patient FALSE . 2 Unclassified_Lachnospiraceae 5.271e-02
SM19 patient FALSE . 2 Unclassified_Lachnospiraceae 1.055e-01
SM2 patient FALSE . 1 Unclassified_Lachnospiraceae 1.097e-02
SM20 1 1 Unclassified_Lachnospiraceae 2.256e-02
SM21 patient FALSE . 1 Unclassified_Lachnospiraceae 5.532e-02
SM22 patient TRUE . 1 Unclassified_Lachnospiraceae 1.113e-01
SM23 patient TRUE . 2 Unclassified_Lachnospiraceae 4.148e-04
SM24 patient FALSE . 1 Unclassified_Lachnospiraceae 1.402e-02
SM25 patient FALSE . 4 Unclassified_Lachnospiraceae 8.430e-02
SM26 1 1 Unclassified_Lachnospiraceae 7.501e-02
SM28 1 1 Unclassified_Lachnospiraceae 9.952e-02
SM29 patient TRUE . 3 Unclassified_Lachnospiraceae 1.128e-02
SM3 patient TRUE . 2 Unclassified_Lachnospiraceae 1.560e-01
SM30 patient TRUE . 4 Unclassified_Lachnospiraceae 3.297e-01
SM31 1 2 Unclassified_Lachnospiraceae 1.294e-02
SM33 patient TRUE . 1 Unclassified_Lachnospiraceae 3.934e-03

(1.1.1.3.3.2.4.2.1.1.1) Widget 40. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.4.2.1.1.1-32337e0ae4dDynamic.Pivot.Table.html

(1.1.1.3.3.2.4.2.1.1.1) Widget 41. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Sample.type.Drug.Before,visit. Click to see HTML widget file in full window: ./1.1.1.3.3.2.4.2.1.1.1-3233347c35dDynamic.Pivot.Table.html

(1.1.1.3.3.2.4.2.1.1.1) Table 40. Summary table. Data grouped by Sample.type.Drug.Before,visit. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.4.2.1.1.1-3233e9c8a68.1.1.1.3.3.2.4.2.1.1.csv

feature Sample.type.Drug.Before visit mean sd median incidence
Bacteroides 1 1 3.125e-01 2.538e-01 3.274e-01 0.94444
Bacteroides 1 2 2.458e-01 2.314e-01 2.458e-01 1.00000
Bacteroides patient FALSE . 1 4.634e-01 3.049e-01 4.392e-01 1.00000
Bacteroides patient FALSE . 2 2.911e-01 2.698e-01 2.221e-01 0.85714
Bacteroides patient FALSE . 3 2.969e-01 3.479e-01 1.684e-01 0.83333
Bacteroides patient FALSE . 4 3.944e-01 2.816e-01 4.205e-01 1.00000
Bacteroides patient TRUE . 1 6.746e-01 2.463e-01 7.735e-01 1.00000
Bacteroides patient TRUE . 2 4.923e-01 3.565e-01 5.141e-01 1.00000
Bacteroides patient TRUE . 3 6.246e-01 2.372e-01 6.382e-01 1.00000
Bacteroides patient TRUE . 4 6.035e-01 2.634e-01 6.589e-01 1.00000
Prevotella 1 1 1.431e-01 2.655e-01 5.869e-04 0.77778
Prevotella 1 2 1.136e-03 6.813e-04 1.136e-03 1.00000
Prevotella patient FALSE . 1 1.134e-01 2.365e-01 4.402e-03 0.80000
Prevotella patient FALSE . 2 1.922e-01 3.252e-01 2.314e-03 0.85714
Prevotella patient FALSE . 3 1.014e-01 2.056e-01 2.378e-04 0.50000
Prevotella patient FALSE . 4 4.440e-03 1.050e-02 1.387e-04 0.50000
Prevotella patient TRUE . 1 4.860e-02 1.305e-01 0.000e+00 0.46154
Prevotella patient TRUE . 2 5.068e-02 1.449e-01 1.416e-04 0.80000
Prevotella patient TRUE . 3 7.740e-03 2.092e-02 1.793e-04 0.62500
Prevotella patient TRUE . 4 5.231e-04 9.932e-04 2.141e-04 0.85714
Unclassified_Lachnospiraceae 1 1 6.389e-02 4.120e-02 6.129e-02 1.00000
Unclassified_Lachnospiraceae 1 2 6.654e-02 7.579e-02 6.654e-02 1.00000
Unclassified_Lachnospiraceae patient FALSE . 1 3.276e-02 3.113e-02 1.269e-02 1.00000
Unclassified_Lachnospiraceae patient FALSE . 2 3.552e-02 3.529e-02 2.075e-02 0.85714
Unclassified_Lachnospiraceae patient FALSE . 3 1.344e-01 1.575e-01 4.278e-02 1.00000
Unclassified_Lachnospiraceae patient FALSE . 4 9.198e-02 4.009e-02 9.333e-02 1.00000
Unclassified_Lachnospiraceae patient TRUE . 1 2.669e-02 3.274e-02 1.049e-02 0.92308
Unclassified_Lachnospiraceae patient TRUE . 2 5.630e-02 7.384e-02 3.288e-02 1.00000
Unclassified_Lachnospiraceae patient TRUE . 3 7.323e-02 8.946e-02 3.982e-02 1.00000
Unclassified_Lachnospiraceae patient TRUE . 4 8.273e-02 1.170e-01 3.912e-02 1.00000
Faecalibacterium 1 1 4.217e-02 4.401e-02 3.575e-02 0.94444
Faecalibacterium 1 2 3.452e-02 4.423e-02 3.452e-02 1.00000
Faecalibacterium patient FALSE . 1 3.876e-02 4.038e-02 2.495e-02 1.00000
Faecalibacterium patient FALSE . 2 7.169e-02 1.285e-01 1.664e-02 0.85714
Faecalibacterium patient FALSE . 3 2.433e-02 2.073e-02 1.749e-02 1.00000
Faecalibacterium patient FALSE . 4 9.878e-02 9.939e-02 6.677e-02 1.00000
Faecalibacterium patient TRUE . 1 1.846e-02 1.438e-02 1.267e-02 0.92308
Faecalibacterium patient TRUE . 2 5.171e-02 1.083e-01 1.129e-02 0.90000
Faecalibacterium patient TRUE . 3 4.364e-02 4.948e-02 2.507e-02 1.00000
Faecalibacterium patient TRUE . 4 3.871e-02 4.144e-02 1.950e-02 1.00000
Lachnospiracea_incertae_sedis 1 1 3.238e-02 2.664e-02 2.788e-02 0.94444
Lachnospiracea_incertae_sedis 1 2 5.683e-02 7.980e-02 5.683e-02 1.00000
Lachnospiracea_incertae_sedis patient FALSE . 1 9.291e-03 8.958e-03 6.378e-03 1.00000
Lachnospiracea_incertae_sedis patient FALSE . 2 1.942e-02 1.950e-02 1.145e-02 0.85714
Lachnospiracea_incertae_sedis patient FALSE . 3 7.174e-02 1.013e-01 1.093e-02 1.00000
Lachnospiracea_incertae_sedis patient FALSE . 4 8.868e-02 6.950e-02 7.666e-02 1.00000
Lachnospiracea_incertae_sedis patient TRUE . 1 1.085e-02 1.317e-02 3.240e-03 0.84615
Lachnospiracea_incertae_sedis patient TRUE . 2 4.535e-02 5.535e-02 2.253e-02 0.90000
Lachnospiracea_incertae_sedis patient TRUE . 3 4.177e-02 4.937e-02 2.248e-02 0.87500
Lachnospiracea_incertae_sedis patient TRUE . 4 2.672e-02 3.288e-02 1.450e-02 0.85714
Parabacteroides 1 1 8.828e-03 8.069e-03 6.610e-03 0.94444
Parabacteroides 1 2 1.807e-02 1.907e-02 1.807e-02 1.00000
Parabacteroides patient FALSE . 1 1.024e-02 1.289e-02 2.166e-03 0.80000
Parabacteroides patient FALSE . 2 2.816e-02 5.131e-02 1.370e-03 0.85714
Parabacteroides patient FALSE . 3 8.124e-03 1.641e-02 0.000e+00 0.33333
Parabacteroides patient FALSE . 4 2.621e-03 5.406e-03 1.849e-04 0.66667
Parabacteroides patient TRUE . 1 5.820e-02 1.381e-01 7.199e-03 0.69231
Parabacteroides patient TRUE . 2 7.576e-02 2.222e-01 5.432e-04 0.80000
Parabacteroides patient TRUE . 3 5.231e-02 7.215e-02 1.782e-02 0.87500
Parabacteroides patient TRUE . 4 6.228e-02 1.228e-01 2.231e-04 0.71429
Alistipes 1 1 4.359e-02 7.436e-02 1.748e-02 0.77778
Alistipes 1 2 6.305e-02 8.361e-02 6.305e-02 1.00000
Alistipes patient FALSE . 1 5.269e-02 7.947e-02 1.928e-02 0.70000
Alistipes patient FALSE . 2 1.185e-02 1.874e-02 6.851e-04 0.57143
Alistipes patient FALSE . 3 8.739e-04 2.141e-03 0.000e+00 0.16667
Alistipes patient FALSE . 4 4.068e-03 8.729e-03 4.160e-04 0.50000
Alistipes patient TRUE . 1 1.696e-02 2.078e-02 9.784e-03 0.69231
Alistipes patient TRUE . 2 2.759e-02 5.265e-02 0.000e+00 0.40000
Alistipes patient TRUE . 3 1.056e-02 2.049e-02 1.516e-03 0.62500
Alistipes patient TRUE . 4 9.648e-03 1.404e-02 2.660e-03 0.57143
Blautia 1 1 2.657e-02 4.449e-02 1.644e-02 1.00000
Blautia 1 2 4.533e-02 6.181e-02 4.533e-02 1.00000
Blautia patient FALSE . 1 1.828e-02 2.097e-02 5.935e-03 1.00000
Blautia patient FALSE . 2 1.872e-02 3.047e-02 2.936e-03 0.85714
Blautia patient FALSE . 3 3.677e-02 3.608e-02 2.566e-02 1.00000
Blautia patient FALSE . 4 1.189e-02 8.838e-03 8.247e-03 1.00000
Blautia patient TRUE . 1 7.798e-03 1.057e-02 3.143e-03 0.92308
Blautia patient TRUE . 2 1.865e-02 3.688e-02 8.351e-03 0.80000
Blautia patient TRUE . 3 1.381e-02 1.440e-02 9.423e-03 1.00000
Blautia patient TRUE . 4 1.700e-02 2.588e-02 6.334e-03 1.00000
Ruminococcus 1 1 5.576e-02 8.722e-02 2.428e-02 0.94444
Ruminococcus 1 2 1.140e-01 1.424e-01 1.140e-01 1.00000
Ruminococcus patient FALSE . 1 4.312e-03 4.547e-03 2.962e-03 1.00000
Ruminococcus patient FALSE . 2 8.027e-03 1.303e-02 1.175e-03 0.57143
Ruminococcus patient FALSE . 3 2.267e-02 3.043e-02 1.710e-02 1.00000
Ruminococcus patient FALSE . 4 1.248e-02 1.947e-02 2.719e-03 0.66667
Ruminococcus patient TRUE . 1 5.840e-03 1.170e-02 1.647e-03 0.84615
Ruminococcus patient TRUE . 2 2.893e-03 2.465e-03 2.473e-03 0.90000
Ruminococcus patient TRUE . 3 2.368e-03 2.385e-03 1.529e-03 0.75000
Ruminococcus patient TRUE . 4 1.994e-03 2.008e-03 1.988e-03 0.85714
Unclassified_Clostridiales 1 1 1.825e-02 2.169e-02 1.279e-02 0.94444
Unclassified_Clostridiales 1 2 3.991e-02 2.040e-02 3.991e-02 1.00000
Unclassified_Clostridiales patient FALSE . 1 1.711e-02 1.800e-02 8.182e-03 1.00000
Unclassified_Clostridiales patient FALSE . 2 1.125e-02 1.229e-02 8.058e-03 0.85714
Unclassified_Clostridiales patient FALSE . 3 5.322e-02 9.895e-02 1.471e-02 1.00000
Unclassified_Clostridiales patient FALSE . 4 2.119e-02 2.066e-02 1.448e-02 1.00000
Unclassified_Clostridiales patient TRUE . 1 6.632e-03 8.900e-03 6.030e-03 1.00000
Unclassified_Clostridiales patient TRUE . 2 8.688e-03 1.226e-02 4.161e-03 0.90000
Unclassified_Clostridiales patient TRUE . 3 1.341e-02 1.283e-02 9.805e-03 1.00000
Unclassified_Clostridiales patient TRUE . 4 6.315e-03 5.937e-03 5.354e-03 1.00000
Lactobacillus 1 1 1.522e-02 6.414e-02 0.000e+00 0.27778
Lactobacillus 1 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus patient FALSE . 1 8.034e-04 1.696e-03 0.000e+00 0.40000
Lactobacillus patient FALSE . 2 1.426e-01 3.768e-01 0.000e+00 0.28571
Lactobacillus patient FALSE . 3 8.881e-04 1.905e-03 2.458e-05 0.50000
Lactobacillus patient FALSE . 4 1.086e-03 2.200e-03 1.609e-04 0.50000
Lactobacillus patient TRUE . 1 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus patient TRUE . 2 1.384e-04 3.240e-04 0.000e+00 0.30000
Lactobacillus patient TRUE . 3 0.000e+00 0.000e+00 0.000e+00 0.00000
Lactobacillus patient TRUE . 4 0.000e+00 0.000e+00 0.000e+00 0.00000
Unclassified_Ruminococcaceae 1 1 3.224e-02 3.357e-02 1.940e-02 0.94444
Unclassified_Ruminococcaceae 1 2 5.710e-02 4.511e-02 5.710e-02 1.00000
Unclassified_Ruminococcaceae patient FALSE . 1 1.774e-02 3.797e-02 5.337e-03 1.00000
Unclassified_Ruminococcaceae patient FALSE . 2 8.976e-03 1.262e-02 3.861e-03 0.85714
Unclassified_Ruminococcaceae patient FALSE . 3 8.313e-03 1.001e-02 4.539e-03 1.00000
Unclassified_Ruminococcaceae patient FALSE . 4 1.269e-02 1.408e-02 7.225e-03 1.00000
Unclassified_Ruminococcaceae patient TRUE . 1 8.291e-03 7.539e-03 6.698e-03 1.00000
Unclassified_Ruminococcaceae patient TRUE . 2 3.945e-03 3.629e-03 2.494e-03 0.90000
Unclassified_Ruminococcaceae patient TRUE . 3 4.088e-03 5.283e-03 2.960e-03 1.00000
Unclassified_Ruminococcaceae patient TRUE . 4 5.241e-03 9.406e-03 2.293e-03 1.00000
Roseburia 1 1 9.054e-03 6.994e-03 6.302e-03 1.00000
Roseburia 1 2 1.069e-02 7.105e-03 1.069e-02 1.00000
Roseburia patient FALSE . 1 7.028e-03 7.428e-03 3.183e-03 1.00000
Roseburia patient FALSE . 2 1.860e-02 3.406e-02 3.861e-03 0.85714
Roseburia patient FALSE . 3 1.395e-02 1.660e-02 9.751e-03 1.00000
Roseburia patient FALSE . 4 5.491e-02 4.492e-02 5.431e-02 1.00000
Roseburia patient TRUE . 1 3.915e-03 5.016e-03 2.110e-03 0.76923
Roseburia patient TRUE . 2 1.514e-02 1.970e-02 6.342e-03 1.00000
Roseburia patient TRUE . 3 1.537e-02 1.691e-02 1.115e-02 1.00000
Roseburia patient TRUE . 4 2.036e-02 2.166e-02 2.208e-02 1.00000
Clostridium_XI 1 1 9.259e-03 1.086e-02 6.425e-03 0.94444
Clostridium_XI 1 2 1.387e-02 8.167e-03 1.387e-02 1.00000
Clostridium_XI patient FALSE . 1 3.278e-02 6.673e-02 3.583e-03 0.90000
Clostridium_XI patient FALSE . 2 4.192e-03 6.009e-03 2.854e-03 0.57143
Clostridium_XI patient FALSE . 3 4.168e-03 5.149e-03 2.607e-03 0.83333
Clostridium_XI patient FALSE . 4 3.122e-02 4.815e-02 1.455e-02 1.00000
Clostridium_XI patient TRUE . 1 5.585e-03 1.194e-02 1.655e-03 0.76923
Clostridium_XI patient TRUE . 2 1.709e-02 4.566e-02 1.260e-03 0.90000
Clostridium_XI patient TRUE . 3 8.726e-03 1.128e-02 2.379e-03 1.00000
Clostridium_XI patient TRUE . 4 1.728e-02 2.154e-02 5.589e-03 1.00000
Enterococcus 1 1 3.133e-03 1.317e-02 0.000e+00 0.16667
Enterococcus 1 2 3.437e-03 4.861e-03 3.437e-03 0.50000
Enterococcus patient FALSE . 1 7.389e-03 2.263e-02 5.447e-05 0.50000
Enterococcus patient FALSE . 2 4.235e-04 6.395e-04 0.000e+00 0.42857
Enterococcus patient FALSE . 3 3.121e-04 7.645e-04 0.000e+00 0.16667
Enterococcus patient FALSE . 4 5.194e-05 1.272e-04 0.000e+00 0.16667
Enterococcus patient TRUE . 1 3.162e-04 9.135e-04 0.000e+00 0.23077
Enterococcus patient TRUE . 2 7.148e-02 2.245e-01 0.000e+00 0.40000
Enterococcus patient TRUE . 3 2.586e-04 4.652e-04 0.000e+00 0.37500
Enterococcus patient TRUE . 4 5.191e-04 9.098e-04 0.000e+00 0.28571
Erysipelotrichaceae_incertae_sedis 1 1 1.177e-03 1.604e-03 6.149e-04 0.77778
Erysipelotrichaceae_incertae_sedis 1 2 8.955e-04 1.223e-04 8.955e-04 1.00000
Erysipelotrichaceae_incertae_sedis patient FALSE . 1 4.282e-02 1.209e-01 1.055e-03 0.80000
Erysipelotrichaceae_incertae_sedis patient FALSE . 2 1.497e-03 2.797e-03 1.957e-04 0.57143
Erysipelotrichaceae_incertae_sedis patient FALSE . 3 1.465e-02 1.880e-02 6.028e-03 1.00000
Erysipelotrichaceae_incertae_sedis patient FALSE . 4 3.076e-02 7.402e-02 2.127e-04 0.66667
Erysipelotrichaceae_incertae_sedis patient TRUE . 1 2.576e-03 3.115e-03 1.373e-03 0.69231
Erysipelotrichaceae_incertae_sedis patient TRUE . 2 1.907e-03 3.034e-03 5.660e-04 1.00000
Erysipelotrichaceae_incertae_sedis patient TRUE . 3 5.662e-03 8.182e-03 2.557e-03 1.00000
Erysipelotrichaceae_incertae_sedis patient TRUE . 4 1.908e-03 1.198e-03 2.231e-03 1.00000
Megamonas 1 1 1.856e-02 5.287e-02 0.000e+00 0.16667
Megamonas 1 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Megamonas patient FALSE . 1 1.089e-05 3.445e-05 0.000e+00 0.10000
Megamonas patient FALSE . 2 4.764e-02 8.486e-02 0.000e+00 0.28571
Megamonas patient FALSE . 3 6.492e-03 1.590e-02 0.000e+00 0.16667
Megamonas patient FALSE . 4 4.717e-03 1.156e-02 0.000e+00 0.16667
Megamonas patient TRUE . 1 3.839e-03 1.384e-02 0.000e+00 0.07692
Megamonas patient TRUE . 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Megamonas patient TRUE . 3 0.000e+00 0.000e+00 0.000e+00 0.00000
Megamonas patient TRUE . 4 2.053e-04 5.432e-04 0.000e+00 0.14286
Sutterella 1 1 1.005e-02 2.746e-02 1.351e-03 0.61111
Sutterella 1 2 0.000e+00 0.000e+00 0.000e+00 0.00000
Sutterella patient FALSE . 1 5.495e-03 1.166e-02 1.302e-04 0.70000
Sutterella patient FALSE . 2 9.702e-03 1.627e-02 0.000e+00 0.42857
Sutterella patient FALSE . 3 6.242e-05 1.529e-04 0.000e+00 0.16667
Sutterella patient FALSE . 4 1.555e-02 3.337e-02 3.219e-04 0.50000
Sutterella patient TRUE . 1 7.355e-03 1.737e-02 0.000e+00 0.38462
Sutterella patient TRUE . 2 5.365e-03 1.176e-02 0.000e+00 0.20000
Sutterella patient TRUE . 3 8.784e-03 1.627e-02 0.000e+00 0.25000
Sutterella patient TRUE . 4 5.578e-03 1.476e-02 0.000e+00 0.14286
Escherichia_Shigella 1 1 1.014e-02 3.951e-02 3.219e-04 0.55556
Escherichia_Shigella 1 2 4.045e-04 5.721e-04 4.045e-04 0.50000
Escherichia_Shigella patient FALSE . 1 1.337e-02 4.052e-02 6.431e-05 0.50000
Escherichia_Shigella patient FALSE . 2 8.508e-04 2.001e-03 0.000e+00 0.42857
Escherichia_Shigella patient FALSE . 3 1.739e-03 1.694e-03 1.798e-03 0.66667
Escherichia_Shigella patient FALSE . 4 2.261e-04 3.197e-04 4.161e-05 0.50000
Escherichia_Shigella patient TRUE . 1 1.466e-02 4.824e-02 0.000e+00 0.30769
Escherichia_Shigella patient TRUE . 2 1.239e-05 2.833e-05 0.000e+00 0.20000
Escherichia_Shigella patient TRUE . 3 2.818e-03 6.836e-03 3.157e-04 0.62500
Escherichia_Shigella patient TRUE . 4 1.381e-02 2.232e-02 1.590e-03 0.57143
Unclassified_Bacteria 1 1 1.364e-02 1.141e-02 1.054e-02 1.00000
Unclassified_Bacteria 1 2 2.617e-02 3.243e-02 2.617e-02 1.00000
Unclassified_Bacteria patient FALSE . 1 1.480e-02 2.717e-02 4.448e-03 1.00000
Unclassified_Bacteria patient FALSE . 2 2.186e-03 2.207e-03 1.388e-03 0.85714
Unclassified_Bacteria patient FALSE . 3 5.270e-03 3.824e-03 3.444e-03 1.00000
Unclassified_Bacteria patient FALSE . 4 4.114e-03 4.251e-03 2.007e-03 1.00000
Unclassified_Bacteria patient TRUE . 1 3.807e-03 4.164e-03 2.257e-03 0.92308
Unclassified_Bacteria patient TRUE . 2 2.145e-03 1.812e-03 2.054e-03 0.90000
Unclassified_Bacteria patient TRUE . 3 1.982e-03 1.537e-03 1.345e-03 1.00000
Unclassified_Bacteria patient TRUE . 4 5.219e-03 8.370e-03 1.399e-03 1.00000

(1.1.1.3.3.2.4.2.1.1.1) Figure 133. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar_stacked plot. Image file: plots/3231fb06f76.svg.

(1.1.1.3.3.2.4.2.1.1.1) Figure 134. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/323257a115b.svg.

(1.1.1.3.3.2.4.2.1.1.1) Figure 135. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/32363bf503d.svg.

(1.1.1.3.3.2.4.2.1.1.1) Figure 136. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/3233842f76e.svg.

(1.1.1.3.3.2.4.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.4.2.1.2.1) Figure 137. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/3237e83f6a.svg.

(1.1.1.3.3.2.4.2.1.2.1) Figure 138. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/3235acec018.svg.

(1.1.1.3.3.2.4.2.1.2.1) Figure 139. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32330bdd2c6.svg.

(1.1.1.3.3.2.4.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.4.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.4.2.2.1.1) Figure 140. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/32377a6bde4.svg.

(1.1.1.3.3.2.4.2.2.1.1) Figure 141. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/323555660f3.svg.

(1.1.1.3.3.2.4.2.2.1.1) Figure 142. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/32313703105.svg.

(1.1.1.3.3.2.4.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.4.2.2.2.1) Figure 143. Abundance. Data grouped by Sample.type.Drug.Before,visit. bar (sample mean) plot. Image file: plots/32370d6df67.svg.

(1.1.1.3.3.2.4.2.2.2.1) Figure 144. Abundance. Data grouped by Sample.type.Drug.Before,visit. violin plot. Image file: plots/323758cd9d1.svg.

(1.1.1.3.3.2.4.2.2.2.1) Figure 145. Abundance. Data grouped by Sample.type.Drug.Before,visit. boxplot plot. Image file: plots/323389dbe37.svg.

(1.1.1.3.3.2.5) Grouping variables Drug.Before.Diet,Sample.type.1
(1.1.1.3.3.2.6) Iterating over Abundance. profile sorting order
(1.1.1.3.3.2.6.1) Abundance. profile sorting order: average abundance
(1.1.1.3.3.2.6.2) Iterating over dodged vs faceted bars

The same data are shown in multiple combinations of graphical representations. This is the same data, but each plot highlights slightly different aspects of it. It is not likely that you will need every plot - pick only what you need.

(1.1.1.3.3.2.6.2.1) faceted plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.6.2.1.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.6.2.1.1.0) Table 41. Data table used for plots. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.6.2.1.1.0-3231b91623.1.1.1.3.3.2.6.2.1.1.csv

.record.id Drug.Before.Diet Sample.type.1 feature Abundance
SM1 DrugBefore_YES patient.before.diet Bacteroides 7.735e-01
SM10 DrugBefore_YES patient.after.diet Bacteroides 2.364e-01
SM100 DrugBefore_YES patient.after.diet Bacteroides 5.420e-01
SM11 DrugBefore_YES patient.after.diet Bacteroides 8.578e-01
SM12 DrugBefore_YES patient.before.diet Bacteroides 8.674e-01
SM13 DrugBefore_NO patient.before.diet Bacteroides 4.295e-01
SM14 DrugBefore_NO patient.before.diet Bacteroides 3.976e-02
SM15 DrugBefore_YES control Bacteroides 4.120e-01
SM16 DrugBefore_NO patient.after.diet Bacteroides 3.890e-01
SM17 DrugBefore_YES patient.before.diet Bacteroides 8.130e-01
SM18 DrugBefore_NO patient.after.diet Bacteroides 6.537e-01
SM19 DrugBefore_NO patient.after.diet Bacteroides 2.221e-01
SM2 DrugBefore_NO patient.before.diet Bacteroides 8.611e-01
SM20 DrugBefore_NO control Bacteroides 3.742e-01
SM21 DrugBefore_NO patient.before.diet Bacteroides 4.490e-01
SM22 DrugBefore_YES patient.before.diet Bacteroides 5.831e-01
SM23 DrugBefore_YES patient.after.diet Bacteroides 2.796e-01
SM24 DrugBefore_NO patient.before.diet Bacteroides 1.435e-01
SM25 DrugBefore_NO patient.after.diet Bacteroides 4.520e-01
SM26 DrugBefore_NO control Bacteroides 5.242e-01
SM28 DrugBefore_NO control Bacteroides 2.194e-01
SM29 DrugBefore_YES patient.after.diet Bacteroides 9.002e-01
SM3 DrugBefore_YES patient.after.diet Bacteroides 2.542e-01
SM30 DrugBefore_YES patient.after.diet Bacteroides 6.581e-02
SM31 DrugBefore_NO control Bacteroides 4.094e-01
SM33 DrugBefore_YES patient.before.diet Bacteroides 1.747e-01
SM35 DrugBefore_NO control Bacteroides 6.247e-01
SM36 DrugBefore_NO patient.after.diet Bacteroides 3.219e-04
SM37 DrugBefore_NO control Bacteroides 3.301e-01
SM38 DrugBefore_YES patient.after.diet Bacteroides 9.828e-01
SM39 DrugBefore_NO patient.before.diet Bacteroides 4.095e-01
SM40 DrugBefore_NO patient.after.diet Bacteroides 6.908e-01
SM41 DrugBefore_YES patient.before.diet Bacteroides 5.037e-01
SM42 DrugBefore_NO patient.after.diet Bacteroides 6.901e-01
SM43 DrugBefore_YES patient.after.diet Bacteroides 6.589e-01
SM44 DrugBefore_NO control Bacteroides 1.150e-02
SM45 DrugBefore_NO patient.after.diet Bacteroides 0.000e+00
SM48 DrugBefore_NO control Bacteroides 3.247e-01
SM49 DrugBefore_YES patient.before.diet Bacteroides 9.292e-01
SM5 DrugBefore_YES patient.after.diet Bacteroides 5.313e-01
SM50 DrugBefore_NO patient.after.diet Bacteroides 0.000e+00
SM51 DrugBefore_YES patient.after.diet Bacteroides 7.122e-01
SM52 DrugBefore_NO patient.before.diet Bacteroides 8.105e-02
SM53 DrugBefore_YES patient.after.diet Bacteroides 3.305e-01
SM54 DrugBefore_YES patient.after.diet Bacteroides 6.239e-01
SM55 DrugBefore_NO control Bacteroides 7.465e-02
SM56 DrugBefore_YES patient.after.diet Bacteroides 1.958e-02
SM57 DrugBefore_YES patient.before.diet Bacteroides 8.679e-01
SM58 DrugBefore_NO patient.after.diet Bacteroides 2.592e-02
SM59 DrugBefore_NO patient.after.diet Bacteroides 5.206e-02
SM60 DrugBefore_YES patient.after.diet Bacteroides 8.428e-01
SM62 DrugBefore_YES patient.before.diet Bacteroides 9.643e-01
SM63 DrugBefore_NO control Bacteroides 5.135e-01
SM64 DrugBefore_YES patient.after.diet Bacteroides 6.977e-01
SM65 DrugBefore_YES patient.after.diet Bacteroides 3.711e-01
SM66 DrugBefore_NO control Bacteroides 6.218e-01
SM67 DrugBefore_YES patient.after.diet Bacteroides 5.778e-01
SM68 DrugBefore_NO patient.after.diet Bacteroides 1.440e-01
SM69 DrugBefore_YES patient.after.diet Bacteroides 8.051e-01
SM7 DrugBefore_NO control Bacteroides 2.126e-01
SM70 DrugBefore_NO control Bacteroides 6.327e-02
SM71 DrugBefore_YES patient.after.diet Bacteroides 8.388e-01
SM72 DrugBefore_NO control Bacteroides 4.762e-03
SM73 DrugBefore_NO patient.before.diet Bacteroides 8.108e-01
SM74 DrugBefore_NO control Bacteroides 8.216e-02
SM75 DrugBefore_NO patient.after.diet Bacteroides 2.377e-03
SM76 DrugBefore_NO control Bacteroides 8.153e-01
SM77 DrugBefore_YES patient.after.diet Bacteroides 7.039e-01
SM79 DrugBefore_NO patient.after.diet Bacteroides 1.173e-01
SM8 DrugBefore_NO patient.before.diet Bacteroides 7.723e-01
SM81 DrugBefore_NO control Bacteroides 0.000e+00
SM82 DrugBefore_YES patient.after.diet Bacteroides 8.624e-01
SM83 DrugBefore_YES patient.before.diet Bacteroides 8.199e-01
SM84 DrugBefore_YES patient.before.diet Bacteroides 2.885e-01
SM86 DrugBefore_YES patient.after.diet Bacteroides 2.482e-03
SM87 DrugBefore_YES patient.before.diet Bacteroides 5.438e-01
SM88 DrugBefore_YES patient.after.diet Bacteroides 7.940e-01
SM89 DrugBefore_NO control Bacteroides 2.115e-03
SM9 DrugBefore_NO patient.after.diet Bacteroides 6.096e-01
SM90 DrugBefore_NO patient.after.diet Bacteroides 4.088e-01
SM91 DrugBefore_YES patient.after.diet Bacteroides 6.525e-01
SM92 DrugBefore_NO patient.after.diet Bacteroides 7.921e-01
SM93 DrugBefore_YES patient.before.diet Bacteroides 6.404e-01
SM95 DrugBefore_NO control Bacteroides 4.955e-01
SM96 DrugBefore_NO patient.before.diet Bacteroides 6.375e-01
SM98 DrugBefore_NO patient.after.diet Bacteroides 2.848e-01
SM99 DrugBefore_NO patient.after.diet Bacteroides 6.503e-01
SM1 DrugBefore_YES patient.before.diet Prevotella 2.598e-04
SM10 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM100 DrugBefore_YES patient.after.diet Prevotella 7.692e-05
SM11 DrugBefore_YES patient.after.diet Prevotella 3.477e-04
SM12 DrugBefore_YES patient.before.diet Prevotella 1.328e-04
SM13 DrugBefore_NO patient.before.diet Prevotella 1.652e-02
SM14 DrugBefore_NO patient.before.diet Prevotella 1.855e-02
SM15 DrugBefore_YES control Prevotella 1.415e-04
SM16 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM17 DrugBefore_YES patient.before.diet Prevotella 4.137e-04
SM18 DrugBefore_NO patient.after.diet Prevotella 3.357e-04
SM19 DrugBefore_NO patient.after.diet Prevotella 2.314e-03
SM2 DrugBefore_NO patient.before.diet Prevotella 2.480e-04
SM20 DrugBefore_NO control Prevotella 0.000e+00
SM21 DrugBefore_NO patient.before.diet Prevotella 0.000e+00
SM22 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM23 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM24 DrugBefore_NO patient.before.diet Prevotella 6.822e-01
SM25 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM26 DrugBefore_NO control Prevotella 2.758e-04
SM28 DrugBefore_NO control Prevotella 3.997e-04
SM29 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM3 DrugBefore_YES patient.after.diet Prevotella 4.458e-02
SM30 DrugBefore_YES patient.after.diet Prevotella 2.762e-03
SM31 DrugBefore_NO control Prevotella 1.618e-03
SM33 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM35 DrugBefore_NO control Prevotella 2.046e-03
SM36 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM37 DrugBefore_NO control Prevotella 7.741e-04
SM38 DrugBefore_YES patient.after.diet Prevotella 1.028e-04
SM39 DrugBefore_NO patient.before.diet Prevotella 4.073e-01
SM40 DrugBefore_NO patient.after.diet Prevotella 2.775e-04
SM41 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM42 DrugBefore_NO patient.after.diet Prevotella 4.994e-04
SM43 DrugBefore_YES patient.after.diet Prevotella 7.452e-05
SM44 DrugBefore_NO control Prevotella 3.227e-01
SM45 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM48 DrugBefore_NO control Prevotella 2.151e-03
SM49 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM5 DrugBefore_YES patient.after.diet Prevotella 5.950e-02
SM50 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM51 DrugBefore_YES patient.after.diet Prevotella 2.231e-04
SM52 DrugBefore_NO patient.before.diet Prevotella 8.062e-03
SM53 DrugBefore_YES patient.after.diet Prevotella 4.611e-01
SM54 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM55 DrugBefore_NO control Prevotella 6.747e-01
SM56 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM57 DrugBefore_YES patient.before.diet Prevotella 3.600e-04
SM58 DrugBefore_NO patient.after.diet Prevotella 6.582e-01
SM59 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM60 DrugBefore_YES patient.after.diet Prevotella 3.404e-04
SM62 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM63 DrugBefore_NO control Prevotella 2.703e-03
SM64 DrugBefore_YES patient.after.diet Prevotella 1.113e-04
SM65 DrugBefore_YES patient.after.diet Prevotella 1.374e-04
SM66 DrugBefore_NO control Prevotella 2.198e-04
SM67 DrugBefore_YES patient.after.diet Prevotella 0.000e+00
SM68 DrugBefore_NO patient.after.diet Prevotella 2.586e-02
SM69 DrugBefore_YES patient.after.diet Prevotella 3.108e-04
SM7 DrugBefore_NO control Prevotella 0.000e+00
SM70 DrugBefore_NO control Prevotella 4.438e-01
SM71 DrugBefore_YES patient.after.diet Prevotella 1.723e-03
SM72 DrugBefore_NO control Prevotella 2.651e-01
SM73 DrugBefore_NO patient.before.diet Prevotella 1.009e-04
SM74 DrugBefore_NO control Prevotella 6.547e-04
SM75 DrugBefore_NO patient.after.diet Prevotella 0.000e+00
SM76 DrugBefore_NO control Prevotella 5.743e-05
SM77 DrugBefore_YES patient.after.diet Prevotella 1.127e-04
SM79 DrugBefore_NO patient.after.diet Prevotella 6.782e-01
SM8 DrugBefore_NO patient.before.diet Prevotella 7.416e-04
SM81 DrugBefore_NO control Prevotella 0.000e+00
SM82 DrugBefore_YES patient.after.diet Prevotella 2.141e-04
SM83 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM84 DrugBefore_YES patient.before.diet Prevotella 4.502e-01
SM86 DrugBefore_YES patient.after.diet Prevotella 3.103e-04
SM87 DrugBefore_YES patient.before.diet Prevotella 1.804e-01
SM88 DrugBefore_YES patient.after.diet Prevotella 1.705e-04
SM89 DrugBefore_NO control Prevotella 8.603e-01
SM9 DrugBefore_NO patient.after.diet Prevotella 8.227e-04
SM90 DrugBefore_NO patient.after.diet Prevotella 5.776e-03
SM91 DrugBefore_YES patient.after.diet Prevotella 2.212e-04
SM92 DrugBefore_NO patient.after.diet Prevotella 9.411e-02
SM93 DrugBefore_YES patient.before.diet Prevotella 0.000e+00
SM95 DrugBefore_NO control Prevotella 0.000e+00
SM96 DrugBefore_NO patient.before.diet Prevotella 0.000e+00
SM98 DrugBefore_NO patient.after.diet Prevotella 5.140e-01
SM99 DrugBefore_NO patient.after.diet Prevotella 4.757e-04
SM1 DrugBefore_YES patient.before.diet Unclassified_Lachnospiraceae 4.529e-02
SM10 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 2.607e-01
SM100 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 1.308e-01
SM11 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 4.404e-03
SM12 DrugBefore_YES patient.before.diet Unclassified_Lachnospiraceae 1.049e-02
SM13 DrugBefore_NO patient.before.diet Unclassified_Lachnospiraceae 1.116e-02
SM14 DrugBefore_NO patient.before.diet Unclassified_Lachnospiraceae 6.172e-02
SM15 DrugBefore_YES control Unclassified_Lachnospiraceae 5.053e-02
SM16 DrugBefore_NO patient.after.diet Unclassified_Lachnospiraceae 1.583e-01
SM17 DrugBefore_YES patient.before.diet Unclassified_Lachnospiraceae 2.938e-02
SM18 DrugBefore_NO patient.after.diet Unclassified_Lachnospiraceae 5.271e-02
SM19 DrugBefore_NO patient.after.diet Unclassified_Lachnospiraceae 1.055e-01
SM2 DrugBefore_NO patient.before.diet Unclassified_Lachnospiraceae 1.097e-02
SM20 DrugBefore_NO control Unclassified_Lachnospiraceae 2.256e-02
SM21 DrugBefore_NO patient.before.diet Unclassified_Lachnospiraceae 5.532e-02
SM22 DrugBefore_YES patient.before.diet Unclassified_Lachnospiraceae 1.113e-01
SM23 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 4.148e-04
SM24 DrugBefore_NO patient.before.diet Unclassified_Lachnospiraceae 1.402e-02
SM25 DrugBefore_NO patient.after.diet Unclassified_Lachnospiraceae 8.430e-02
SM26 DrugBefore_NO control Unclassified_Lachnospiraceae 7.501e-02
SM28 DrugBefore_NO control Unclassified_Lachnospiraceae 9.952e-02
SM29 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 1.128e-02
SM3 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 1.560e-01
SM30 DrugBefore_YES patient.after.diet Unclassified_Lachnospiraceae 3.297e-01
SM31 DrugBefore_NO control Unclassified_Lachnospiraceae 1.294e-02
SM33 DrugBefore_YES patient.before.diet Unclassified_Lachnospiraceae 3.934e-03

(1.1.1.3.3.2.6.2.1.1.1) Widget 42. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Stacked Bar Chart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.3.3.2.6.2.1.1.1-3237181ba1Dynamic.Pivot.Table.html

(1.1.1.3.3.2.6.2.1.1.1) Widget 43. Dynamic Pivot Table link (drag and drop field names and pick averaging functions or plot types; click on fields or legend elements to filter values). Starting rendering is Table Barchart. Data grouped by Drug.Before.Diet,Sample.type.1. Click to see HTML widget file in full window: ./1.1.1.3.3.2.6.2.1.1.1-323675ab292Dynamic.Pivot.Table.html

(1.1.1.3.3.2.6.2.1.1.1) Table 42. Summary table. Data grouped by Drug.Before.Diet,Sample.type.1. Showing only 200 first rows. Full dataset is also saved in a delimited text file (click to download and open e.g. in Excel) data/1.1.1.3.3.2.6.2.1.1.1-3233e26e853.1.1.1.3.3.2.6.2.1.1.csv

feature Drug.Before.Diet Sample.type.1 mean sd median incidence
Bacteroides DrugBefore_NO control 3.002e-01 2.522e-01 3.247e-01 0.94737
Bacteroides DrugBefore_NO patient.after.diet 3.255e-01 2.868e-01 2.848e-01 0.89474
Bacteroides DrugBefore_NO patient.before.diet 4.634e-01 3.049e-01 4.392e-01 1.00000
Bacteroides DrugBefore_YES control 4.120e-01 NA 4.120e-01 1.00000
Bacteroides DrugBefore_YES patient.after.diet 5.657e-01 2.919e-01 6.525e-01 1.00000
Bacteroides DrugBefore_YES patient.before.diet 6.746e-01 2.463e-01 7.735e-01 1.00000
Prevotella DrugBefore_NO control 1.357e-01 2.600e-01 7.741e-04 0.78947
Prevotella DrugBefore_NO patient.after.diet 1.043e-01 2.310e-01 4.757e-04 0.63158
Prevotella DrugBefore_NO patient.before.diet 1.134e-01 2.365e-01 4.402e-03 0.80000
Prevotella DrugBefore_YES control 1.415e-04 NA 1.415e-04 1.00000
Prevotella DrugBefore_YES patient.after.diet 2.290e-02 9.243e-02 1.705e-04 0.76000
Prevotella DrugBefore_YES patient.before.diet 4.860e-02 1.305e-01 0.000e+00 0.46154
Unclassified_Lachnospiraceae DrugBefore_NO control 6.487e-02 4.373e-02 6.396e-02 1.00000
Unclassified_Lachnospiraceae DrugBefore_NO patient.after.diet 8.458e-02 9.765e-02 4.930e-02 0.94737
Unclassified_Lachnospiraceae DrugBefore_NO patient.before.diet 3.276e-02 3.113e-02 1.269e-02 1.00000
Unclassified_Lachnospiraceae DrugBefore_YES control 5.053e-02 NA 5.053e-02 1.00000
Unclassified_Lachnospiraceae DrugBefore_YES patient.after.diet 6.912e-02 8.904e-02 3.912e-02 1.00000
Unclassified_Lachnospiraceae DrugBefore_YES patient.before.diet 2.669e-02 3.274e-02 1.049e-02 0.92308
Faecalibacterium DrugBefore_NO control 4.161e-02 4.407e-02 3.571e-02 0.94737
Faecalibacterium DrugBefore_NO patient.after.diet 6.529e-02 9.654e-02 1.901e-02 0.94737
Faecalibacterium DrugBefore_NO patient.before.diet 3.876e-02 4.038e-02 2.495e-02 1.00000
Faecalibacterium DrugBefore_YES control 3.751e-02 NA 3.751e-02 1.00000
Faecalibacterium DrugBefore_YES patient.after.diet 4.549e-02 7.464e-02 1.950e-02 0.96000
Faecalibacterium DrugBefore_YES patient.before.diet 1.846e-02 1.438e-02 1.267e-02 0.92308
Lachnospiracea_incertae_sedis DrugBefore_NO control 3.487e-02 3.292e-02 2.398e-02 0.94737
Lachnospiracea_incertae_sedis DrugBefore_NO patient.after.diet 5.781e-02 7.262e-02 2.770e-02 0.94737
Lachnospiracea_incertae_sedis DrugBefore_NO patient.before.diet 9.291e-03 8.958e-03 6.378e-03 1.00000
Lachnospiracea_incertae_sedis DrugBefore_YES control 3.397e-02 NA 3.397e-02 1.00000
Lachnospiracea_incertae_sedis DrugBefore_YES patient.after.diet 3.899e-02 4.683e-02 2.079e-02 0.88000
Lachnospiracea_incertae_sedis DrugBefore_YES patient.before.diet 1.085e-02 1.317e-02 3.240e-03 0.84615
Parabacteroides DrugBefore_NO control 1.016e-02 9.315e-03 7.497e-03 0.94737
Parabacteroides DrugBefore_NO patient.after.diet 1.377e-02 3.306e-02 4.114e-04 0.63158
Parabacteroides DrugBefore_NO patient.before.diet 1.024e-02 1.289e-02 2.166e-03 0.80000
Parabacteroides DrugBefore_YES control 2.052e-03 NA 2.052e-03 1.00000
Parabacteroides DrugBefore_YES patient.after.diet 6.448e-02 1.546e-01 1.021e-03 0.80000
Parabacteroides DrugBefore_YES patient.before.diet 5.820e-02 1.381e-01 7.199e-03 0.69231
Alistipes DrugBefore_NO control 4.456e-02 7.502e-02 1.418e-02 0.78947
Alistipes DrugBefore_NO patient.after.diet 5.926e-03 1.276e-02 0.000e+00 0.42105
Alistipes DrugBefore_NO patient.before.diet 5.269e-02 7.947e-02 1.928e-02 0.70000
Alistipes DrugBefore_YES control 6.419e-02 NA 6.419e-02 1.00000
Alistipes DrugBefore_YES patient.after.diet 1.712e-02 3.588e-02 1.695e-04 0.52000
Alistipes DrugBefore_YES patient.before.diet 1.696e-02 2.078e-02 9.784e-03 0.69231
Blautia DrugBefore_NO control 2.865e-02 4.600e-02 1.538e-02 1.00000
Blautia DrugBefore_NO patient.after.diet 2.226e-02 2.835e-02 6.232e-03 0.94737
Blautia DrugBefore_NO patient.before.diet 1.828e-02 2.097e-02 5.935e-03 1.00000
Blautia DrugBefore_YES control 2.456e-02 NA 2.456e-02 1.00000
Blautia DrugBefore_YES patient.after.diet 1.664e-02 2.725e-02 7.161e-03 0.92000
Blautia DrugBefore_YES patient.before.diet 7.798e-03 1.057e-02 3.143e-03 0.92308
Ruminococcus DrugBefore_NO control 5.365e-02 8.556e-02 1.987e-02 0.94737
Ruminococcus DrugBefore_NO patient.after.diet 1.406e-02 2.142e-02 1.851e-03 0.73684
Ruminococcus DrugBefore_NO patient.before.diet 4.312e-03 4.547e-03 2.962e-03 1.00000
Ruminococcus DrugBefore_YES control 2.124e-01 NA 2.124e-01 1.00000
Ruminococcus DrugBefore_YES patient.after.diet 2.473e-03 2.256e-03 1.958e-03 0.84000
Ruminococcus DrugBefore_YES patient.before.diet 5.840e-03 1.170e-02 1.647e-03 0.84615
Unclassified_Clostridiales DrugBefore_NO control 2.061e-02 2.267e-02 1.397e-02 0.94737
Unclassified_Clostridiales DrugBefore_NO patient.after.diet 2.764e-02 5.679e-02 1.332e-02 0.94737
Unclassified_Clostridiales DrugBefore_NO patient.before.diet 1.711e-02 1.800e-02 8.182e-03 1.00000
Unclassified_Clostridiales DrugBefore_YES control 1.677e-02 NA 1.677e-02 1.00000
Unclassified_Clostridiales DrugBefore_YES patient.after.diet 9.534e-03 1.102e-02 6.365e-03 0.96000
Unclassified_Clostridiales DrugBefore_YES patient.before.diet 6.632e-03 8.900e-03 6.030e-03 1.00000
Lactobacillus DrugBefore_NO control 1.441e-02 6.243e-02 0.000e+00 0.21053
Lactobacillus DrugBefore_NO patient.after.diet 5.315e-02 2.286e-01 0.000e+00 0.42105
Lactobacillus DrugBefore_NO patient.before.diet 8.034e-04 1.696e-03 0.000e+00 0.40000
Lactobacillus DrugBefore_YES control 7.077e-05 NA 7.077e-05 1.00000
Lactobacillus DrugBefore_YES patient.after.diet 5.537e-05 2.101e-04 0.000e+00 0.12000
Lactobacillus DrugBefore_YES patient.before.diet 0.000e+00 0.000e+00 0.000e+00 0.00000
Unclassified_Ruminococcaceae DrugBefore_NO control 3.356e-02 3.478e-02 1.988e-02 0.94737
Unclassified_Ruminococcaceae DrugBefore_NO patient.after.diet 9.938e-03 1.182e-02 3.861e-03 0.94737
Unclassified_Ruminococcaceae DrugBefore_NO patient.before.diet 1.774e-02 3.797e-02 5.337e-03 1.00000
Unclassified_Ruminococcaceae DrugBefore_YES control 5.697e-02 NA 5.697e-02 1.00000
Unclassified_Ruminococcaceae DrugBefore_YES patient.after.diet 4.353e-03 5.960e-03 2.538e-03 0.96000
Unclassified_Ruminococcaceae DrugBefore_YES patient.before.diet 8.291e-03 7.539e-03 6.698e-03 1.00000
Roseburia DrugBefore_NO control 9.371e-03 6.984e-03 6.306e-03 1.00000
Roseburia DrugBefore_NO patient.after.diet 2.860e-02 3.695e-02 1.223e-02 0.94737
Roseburia DrugBefore_NO patient.before.diet 7.028e-03 7.428e-03 3.183e-03 1.00000
Roseburia DrugBefore_YES control 6.298e-03 NA 6.298e-03 1.00000
Roseburia DrugBefore_YES patient.after.diet 1.667e-02 1.876e-02 1.106e-02 1.00000
Roseburia DrugBefore_YES patient.before.diet 3.915e-03 5.016e-03 2.110e-03 0.76923
Clostridium_XI DrugBefore_NO control 9.713e-03 1.083e-02 6.454e-03 0.94737
Clostridium_XI DrugBefore_NO patient.after.diet 1.272e-02 2.881e-02 4.519e-03 0.78947
Clostridium_XI DrugBefore_NO patient.before.diet 3.278e-02 6.673e-02 3.583e-03 0.90000
Clostridium_XI DrugBefore_YES control 9.837e-03 NA 9.837e-03 1.00000
Clostridium_XI DrugBefore_YES patient.after.diet 1.447e-02 3.084e-02 3.419e-03 0.96000
Clostridium_XI DrugBefore_YES patient.before.diet 5.585e-03 1.194e-02 1.655e-03 0.76923
Enterococcus DrugBefore_NO control 3.330e-03 1.283e-02 0.000e+00 0.21053
Enterococcus DrugBefore_NO patient.after.diet 2.710e-04 5.734e-04 0.000e+00 0.26316
Enterococcus DrugBefore_NO patient.before.diet 7.389e-03 2.263e-02 5.447e-05 0.50000
Enterococcus DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Enterococcus DrugBefore_YES patient.after.diet 2.882e-02 1.420e-01 0.000e+00 0.36000
Enterococcus DrugBefore_YES patient.before.diet 3.162e-04 9.135e-04 0.000e+00 0.23077
Erysipelotrichaceae_incertae_sedis DrugBefore_NO control 1.183e-03 1.554e-03 8.091e-04 0.78947
Erysipelotrichaceae_incertae_sedis DrugBefore_NO patient.after.diet 1.489e-02 4.215e-02 3.329e-04 0.73684
Erysipelotrichaceae_incertae_sedis DrugBefore_NO patient.before.diet 4.282e-02 1.209e-01 1.055e-03 0.80000
Erysipelotrichaceae_incertae_sedis DrugBefore_YES control 4.954e-04 NA 4.954e-04 1.00000
Erysipelotrichaceae_incertae_sedis DrugBefore_YES patient.after.diet 3.109e-03 5.151e-03 1.236e-03 1.00000
Erysipelotrichaceae_incertae_sedis DrugBefore_YES patient.before.diet 2.576e-03 3.115e-03 1.373e-03 0.69231
Megamonas DrugBefore_NO control 1.758e-02 5.155e-02 0.000e+00 0.15789
Megamonas DrugBefore_NO patient.after.diet 2.109e-02 5.424e-02 0.000e+00 0.21053
Megamonas DrugBefore_NO patient.before.diet 1.089e-05 3.445e-05 0.000e+00 0.10000
Megamonas DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Megamonas DrugBefore_YES patient.after.diet 5.749e-05 2.874e-04 0.000e+00 0.04000
Megamonas DrugBefore_YES patient.before.diet 3.839e-03 1.384e-02 0.000e+00 0.07692
Sutterella DrugBefore_NO control 9.518e-03 2.678e-02 1.291e-03 0.57895
Sutterella DrugBefore_NO patient.after.diet 8.504e-03 2.094e-02 0.000e+00 0.36842
Sutterella DrugBefore_NO patient.before.diet 5.495e-03 1.166e-02 1.302e-04 0.70000
Sutterella DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Sutterella DrugBefore_YES patient.after.diet 6.519e-03 1.364e-02 0.000e+00 0.20000
Sutterella DrugBefore_YES patient.before.diet 7.355e-03 1.737e-02 0.000e+00 0.38462
Escherichia_Shigella DrugBefore_NO control 9.648e-03 3.846e-02 3.570e-04 0.57895
Escherichia_Shigella DrugBefore_NO patient.after.diet 9.340e-04 1.596e-03 8.323e-05 0.52632
Escherichia_Shigella DrugBefore_NO patient.before.diet 1.337e-02 4.052e-02 6.431e-05 0.50000
Escherichia_Shigella DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Escherichia_Shigella DrugBefore_YES patient.after.diet 4.775e-03 1.314e-02 0.000e+00 0.44000
Escherichia_Shigella DrugBefore_YES patient.before.diet 1.466e-02 4.824e-02 0.000e+00 0.30769
Unclassified_Bacteria DrugBefore_NO control 1.534e-02 1.388e-02 1.188e-02 1.00000
Unclassified_Bacteria DrugBefore_NO patient.after.diet 3.769e-03 3.531e-03 2.600e-03 0.94737
Unclassified_Bacteria DrugBefore_NO patient.before.diet 1.480e-02 2.717e-02 4.448e-03 1.00000
Unclassified_Bacteria DrugBefore_YES control 6.298e-03 NA 6.298e-03 1.00000
Unclassified_Bacteria DrugBefore_YES patient.after.diet 2.953e-03 4.639e-03 1.726e-03 0.96000
Unclassified_Bacteria DrugBefore_YES patient.before.diet 3.807e-03 4.164e-03 2.257e-03 0.92308
Clostridium_IV DrugBefore_NO control 1.939e-02 3.023e-02 7.943e-03 0.94737
Clostridium_IV DrugBefore_NO patient.after.diet 3.574e-03 8.999e-03 2.630e-04 0.57895
Clostridium_IV DrugBefore_NO patient.before.diet 4.399e-03 7.693e-03 1.573e-03 0.90000
Clostridium_IV DrugBefore_YES control 2.201e-02 NA 2.201e-02 1.00000
Clostridium_IV DrugBefore_YES patient.after.diet 1.737e-03 3.154e-03 3.917e-04 0.68000
Clostridium_IV DrugBefore_YES patient.before.diet 5.740e-03 9.719e-03 1.461e-03 0.76923
Clostridium_XlVa DrugBefore_NO control 8.527e-03 1.214e-02 4.382e-03 0.94737
Clostridium_XlVa DrugBefore_NO patient.after.diet 7.430e-03 1.314e-02 4.075e-03 0.94737
Clostridium_XlVa DrugBefore_NO patient.before.diet 8.294e-03 1.001e-02 4.344e-03 1.00000
Clostridium_XlVa DrugBefore_YES control 4.600e-03 NA 4.600e-03 1.00000
Clostridium_XlVa DrugBefore_YES patient.after.diet 5.389e-03 7.418e-03 2.723e-03 0.96000
Clostridium_XlVa DrugBefore_YES patient.before.diet 4.560e-03 3.747e-03 5.758e-03 0.92308
Unclassified_Firmicutes DrugBefore_NO control 8.481e-03 1.082e-02 3.610e-03 1.00000
Unclassified_Firmicutes DrugBefore_NO patient.after.diet 1.279e-02 1.641e-02 7.867e-03 0.89474
Unclassified_Firmicutes DrugBefore_NO patient.before.diet 2.802e-03 4.001e-03 1.172e-03 1.00000
Unclassified_Firmicutes DrugBefore_YES control 8.704e-03 NA 8.704e-03 1.00000
Unclassified_Firmicutes DrugBefore_YES patient.after.diet 1.393e-03 1.599e-03 7.834e-04 0.88000
Unclassified_Firmicutes DrugBefore_YES patient.before.diet 2.142e-03 2.989e-03 6.030e-04 0.76923
Haemophilus DrugBefore_NO control 1.345e-03 2.373e-03 3.570e-04 0.68421
Haemophilus DrugBefore_NO patient.after.diet 1.030e-02 2.473e-02 1.077e-03 0.63158
Haemophilus DrugBefore_NO patient.before.diet 1.089e-03 2.532e-03 0.000e+00 0.40000
Haemophilus DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Haemophilus DrugBefore_YES patient.after.diet 8.384e-03 3.455e-02 1.554e-04 0.60000
Haemophilus DrugBefore_YES patient.before.diet 1.341e-04 2.383e-04 0.000e+00 0.30769
Bifidobacterium DrugBefore_NO control 1.554e-02 4.372e-02 1.599e-03 0.84211
Bifidobacterium DrugBefore_NO patient.after.diet 1.118e-03 2.756e-03 0.000e+00 0.47368
Bifidobacterium DrugBefore_NO patient.before.diet 1.552e-03 3.211e-03 1.985e-04 0.70000
Bifidobacterium DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Bifidobacterium DrugBefore_YES patient.after.diet 3.146e-03 6.118e-03 2.227e-04 0.64000
Bifidobacterium DrugBefore_YES patient.before.diet 1.974e-03 5.715e-03 3.015e-04 0.61538
Dorea DrugBefore_NO control 8.553e-03 8.887e-03 5.372e-03 0.94737
Dorea DrugBefore_NO patient.after.diet 4.478e-03 7.248e-03 1.387e-03 0.89474
Dorea DrugBefore_NO patient.before.diet 7.990e-03 1.330e-02 4.205e-03 1.00000
Dorea DrugBefore_YES control 5.307e-03 NA 5.307e-03 1.00000
Dorea DrugBefore_YES patient.after.diet 2.468e-03 6.676e-03 5.754e-04 0.84000
Dorea DrugBefore_YES patient.before.diet 2.561e-03 4.804e-03 3.600e-04 0.53846
Unclassified_Bacteroidales DrugBefore_NO control 2.240e-03 3.807e-03 1.343e-03 0.84211
Unclassified_Bacteroidales DrugBefore_NO patient.after.diet 7.569e-03 1.940e-02 4.994e-04 0.63158
Unclassified_Bacteroidales DrugBefore_NO patient.before.diet 3.923e-03 7.636e-03 1.341e-03 1.00000
Unclassified_Bacteroidales DrugBefore_YES control 7.077e-05 NA 7.077e-05 1.00000
Unclassified_Bacteroidales DrugBefore_YES patient.after.diet 2.614e-03 2.295e-03 2.060e-03 0.92000
Unclassified_Bacteroidales DrugBefore_YES patient.before.diet 8.234e-03 1.716e-02 3.015e-03 1.00000
Clostridium_XVIII DrugBefore_NO control 4.550e-03 1.002e-02 1.206e-03 0.89474
Clostridium_XVIII DrugBefore_NO patient.after.diet 9.265e-03 1.850e-02 1.109e-03 0.78947
Clostridium_XVIII DrugBefore_NO patient.before.diet 3.441e-03 3.257e-03 1.827e-03 1.00000
Clostridium_XVIII DrugBefore_YES control 1.628e-03 NA 1.628e-03 1.00000
Clostridium_XVIII DrugBefore_YES patient.after.diet 1.329e-03 1.855e-03 5.301e-04 0.84000
Clostridium_XVIII DrugBefore_YES patient.before.diet 3.688e-03 4.942e-03 1.574e-03 0.76923
Akkermansia DrugBefore_NO control 4.665e-03 1.033e-02 0.000e+00 0.47368
Akkermansia DrugBefore_NO patient.after.diet 2.306e-04 6.964e-04 0.000e+00 0.15789
Akkermansia DrugBefore_NO patient.before.diet 6.661e-03 1.204e-02 0.000e+00 0.40000
Akkermansia DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Akkermansia DrugBefore_YES patient.after.diet 4.256e-04 1.542e-03 0.000e+00 0.08000
Akkermansia DrugBefore_YES patient.before.diet 1.355e-02 4.857e-02 0.000e+00 0.30769
Veillonella DrugBefore_NO control 1.367e-03 5.050e-03 0.000e+00 0.31579
Veillonella DrugBefore_NO patient.after.diet 8.798e-03 2.114e-02 4.125e-04 0.78947
Veillonella DrugBefore_NO patient.before.diet 2.015e-03 5.427e-03 3.100e-05 0.50000
Veillonella DrugBefore_YES control 7.077e-05 NA 7.077e-05 1.00000
Veillonella DrugBefore_YES patient.after.diet 3.255e-03 1.378e-02 7.372e-05 0.56000
Veillonella DrugBefore_YES patient.before.diet 3.865e-04 7.773e-04 0.000e+00 0.46154
Streptococcus DrugBefore_NO control 5.231e-03 1.739e-02 4.401e-04 0.78947
Streptococcus DrugBefore_NO patient.after.diet 5.346e-03 1.406e-02 4.893e-04 0.84211
Streptococcus DrugBefore_NO patient.before.diet 3.878e-03 6.983e-03 3.720e-04 0.80000
Streptococcus DrugBefore_YES control 1.486e-03 NA 1.486e-03 1.00000
Streptococcus DrugBefore_YES patient.after.diet 9.295e-04 2.011e-03 2.231e-04 0.72000
Streptococcus DrugBefore_YES patient.before.diet 7.915e-04 1.487e-03 9.707e-05 0.61538
Clostridium_sensu_stricto DrugBefore_NO control 3.324e-03 7.090e-03 4.401e-04 0.78947
Clostridium_sensu_stricto DrugBefore_NO patient.after.diet 4.790e-03 9.826e-03 5.550e-04 0.57895
Clostridium_sensu_stricto DrugBefore_NO patient.before.diet 3.645e-03 8.701e-03 1.769e-04 0.70000
Clostridium_sensu_stricto DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Clostridium_sensu_stricto DrugBefore_YES patient.after.diet 1.606e-03 4.437e-03 0.000e+00 0.48000
Clostridium_sensu_stricto DrugBefore_YES patient.before.diet 3.112e-03 6.198e-03 0.000e+00 0.38462
Unclassified_Clostridiaceae_1 DrugBefore_NO control 6.780e-04 1.364e-03 7.326e-05 0.57895
Unclassified_Clostridiaceae_1 DrugBefore_NO patient.after.diet 1.130e-02 3.026e-02 4.125e-04 0.57895
Unclassified_Clostridiaceae_1 DrugBefore_NO patient.before.diet 4.953e-04 8.802e-04 8.846e-05 0.60000
Unclassified_Clostridiaceae_1 DrugBefore_YES control 0.000e+00 NA 0.000e+00 0.00000
Unclassified_Clostridiaceae_1 DrugBefore_YES patient.after.diet 5.280e-04 1.803e-03 0.000e+00 0.40000
Unclassified_Clostridiaceae_1 DrugBefore_YES patient.before.diet 1.058e-04 3.561e-04 0.000e+00 0.15385
Klebsiella DrugBefore_NO control 4.860e-03 2.093e-02 0.000e+00 0.15789
Klebsiella DrugBefore_NO patient.after.diet 3.340e-03 1.243e-02 0.000e+00 0.31579

(1.1.1.3.3.2.6.2.1.1.1) Figure 146. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar_stacked plot. Image file: plots/3236f7baf87.svg.

(1.1.1.3.3.2.6.2.1.1.1) Figure 147. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/323697b7c22.svg.

(1.1.1.3.3.2.6.2.1.1.1) Figure 148. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3232f8662a4.svg.

(1.1.1.3.3.2.6.2.1.1.1) Figure 149. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32377b02037.svg.

(1.1.1.3.3.2.6.2.1.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.6.2.1.2.1) Figure 150. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/323b79b753.svg.

(1.1.1.3.3.2.6.2.1.2.1) Figure 151. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/3235147260d.svg.

(1.1.1.3.3.2.6.2.1.2.1) Figure 152. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/32324776066.svg.

(1.1.1.3.3.2.6.2.2) dodged plots. Iterating over orientation and, optionally, scaling
(1.1.1.3.3.2.6.2.2.1) Abundance. Plot is in original orientation, Y axis SQRT scaled. Iterating over plot geometry

(1.1.1.3.3.2.6.2.2.1.1) Figure 153. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3231de23e2d.svg.

(1.1.1.3.3.2.6.2.2.1.1) Figure 154. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/323777b3a64.svg.

(1.1.1.3.3.2.6.2.2.1.1) Figure 155. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3232aaa2990.svg.

(1.1.1.3.3.2.6.2.2.2) Abundance. Plot is in flipped orientation, Y axis not scaled. Iterating over plot geometry

(1.1.1.3.3.2.6.2.2.2.1) Figure 156. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. bar (sample mean) plot. Image file: plots/3237b4205ee.svg.

(1.1.1.3.3.2.6.2.2.2.1) Figure 157. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. violin plot. Image file: plots/323214c0cb5.svg.

(1.1.1.3.3.2.6.2.2.2.1) Figure 158. Abundance. Data grouped by Drug.Before.Diet,Sample.type.1. boxplot plot. Image file: plots/3235a35bc1a.svg.

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